Test data for AUTOSTRUCT and beyond

	AUTOSTRUCT - TEST DATA

AUTOSTRUCT	AUTOSTRUCT - TEST DATA	More test data	Contact

At the Autostruct Coordination Meeting 4 in Amsterdam on 25-MAR-2002, the process to get a collection of test data together was set in motion. The data are to be kept on the Autostruct website for everyone (Autostruct, but also the wider community - Phenix for instance) to use. The test data will have various purposes:

to test programs are correctly installed;
to build tutorials;
ability to generate synthetic data with an arbitrary noise level from any PDB file. Initially assuming MAD/SAD/SeMET, although in the long run MIR/SIR would be nice too (request from Kevin, especially necessary for automation work);

We will endeavor to gather native as well as additional data (i.e. SAD, MAD, derivatives).

Test data already in use:

molecule name	details, (potential) use	spacegroup	resolution (Å)	data	PDB code	PDB SF code
ModE	Hall et al. SHELX test data; MAD reflection file contains _refln.F_meas_au and _refln.F_meas_sigma_au at 4 wavelengths	P2₁2₁2	1.75	sfdata-mode.tgz tar -xvzf ./sfdata-mode.tgz to unpack into directory sfdata/ sfdata-mode.tgz contains mode-1b9m-std.mtz with columns FP SIGFP FC PHIC FWT PHWT DELFWT PHDELWT FOM	1B9M	r1b9msf
JIA (Acyl-CoA Thioesterase II)	Li et al. SHELX test data; MAD reflection file at PDB contains _refln.intensity_meas and _refln.intensity_sigma	C222₁	1.90	sfdata-jia.tgz tar -xvzf ./sfdata-jia.tgz to unpack into directory sfdata/ sfdata-jia.tgz contains: jia_readme.txt with some data collection information jia.hkl with native S-Met data jia_hrem.sca, jia_peak.sca, jia_infl.sca, jia_lrem.sca with Se-Met MAD data jia_1c8u.pdb with S-Met model at PDB jia-1c8u-std.mtz with columns FP SIGFP FC PHIC FWT PHWT DELFWT PHDELWT FOM	1C8U	r1c8usf
RRF	Selmer et al. SHELX test data reflection file contains _refln.F_meas_au and _refln.F_meas_sigma_au	P4₃2₁2	2.55	sfdata-rrf.tgz tar -xvzf ./sfdata-rrf.tgz to unpack into directory sfdata/ sfdata-rrf.tgz contains rrf-1dd5-std.mtz with columns FP SIGFP FC PHIC FWT PHWT DELFWT PHDELWT FOM	1DD5	r1dd5sf
TransH	Buckley et al. SHELX test data reflection data not released yet	P2₁	2.00		1F8G
Cyanase	Walsh et al. SHELX test data; MAD 30Se reflection file at PDB contains _refln.F_meas and _refln.F_meas_sigma	P1	1.65	sfdata-cynsemet.tgz tar -xvzf ./sfdata-cynsemet.tgz to unpack into directory sfdata/ sfdata-cynsemet.tgz contains: cynsemet.mtz with native data to 1.65Å (collected at 1.0332Å) and 4 wavelength MAD data to 2.4Å (wavelengths: 1 = low-energy remote = 1.0781Å, 2 = inflection point = 0.9795Å, 3 = peak = 0.9793Å, 4 = high-energy remote = 0.9465Å) with columns DANO and F⁺/F^- cynsemet-1dw9-std.mtz with columns FP SIGFP FC PHIC FWT PHWT DELFWT PHDELWT FOM	1DW9	r1dw9sf
Thaumatin	Debreczeni et al. SHELX test data; SAD,SIRAS reflection file at PDB contains _refln.F_meas_au and _refln.F_meas_sigma_au, data collected in 1994 to 1.75Å resolution	P4₁2₁2	1.55	sfdata-thau.tgz tar -xvzf ./sfdata-thau.tgz to unpack into directory sfdata/ sfdata-thau.tgz contains: thau-nat.hkl with native data (1.55Å resolution, collected at 1.54Å) thau-iod.hkl data for iodide derivative (2.0Å resolution, collected at 1.54Å) thau-sad - SHELX command script for SAD thau-siras - SHELX command script for SIRAS	1THW	r1thwsf
Cubic insulin	Sheldrick SHELX test data, synchrotron test data very fast data collection possible to high resolution 6 sulfurs can be found easily by SAD phasing	I2₁3	1.35	sfdata-cubins.tgz tar -xvzf ./sfdata-cubins.tgz to unpack into directory sfdata/ sfdata-cubins.tgz contains cubins.sca with columns I and SIGI for centric reflections, and I(+)/SIGI(+) and I(-)/SIGI(-) for acentric reflections
various	other test data and tutorial material for SHELX on the SHELX Program Page, especially from the 'List of files on ftp site & CD'
RNAse Sa	Sevcik et al. CCP4 test data; MIR, refinement reflection file at PDB contains _refln.intensity_meas and _refln.intensity_sigma; coordinate file at PDB contains ANISOU	P2₁2₁2₁	2.5, 1.8 and 1.15	sfdata-rnase.tgz tar -xvzf ./sfdata-rnase.tgz to unpack into directory sfdata/ sfdata-rnase.tgz contains: rnase25.mtz - 2.5Å data for HG, PT and I derivatives (including DANO); fairly poor (old) derivative data, useful for MIR test/tutorial rnase18.mtz - 1.8Å data for guanosine phosphate complexes; fairly poor (old) data, used for refinement tutorial for liganded proteins; columns FNAT SIGFNAT FreeR_flag F3GP SIGF3GP F2GP SIGF2GP rnase115.mtz - 1.15Å data for refinement; columns FP SIGFP FC PHIC	1LNI	r1lnisf
GerE	Ducros et al. CCP4 test data; MAD no SF data available at PDB 2.75Å MAD data set with associated native to 2.15Å	C2	2.15	sfdata-gere.tgz tar -xvzf ./sfdata-gere.tgz to unpack into directory sfdata/ sfdata-gere.tgz contains: gere_nat.sca with native data (collected at 0.870Å) gere_hrm.mtz, gere_peak.mtz, gere_infl.mtz, gere_lrm.mtz with anomalous data (DANO and F⁺/F^-) for 4 wavelengths (0.8865, 0.9793, 0.9795 and 0.9797Å respectively)	1FSE
Toxd	Skarzynski CCP4 test data small data set reflection file at PDB contains _refln.F_meas_au and _refln.F_meas_sigma_au other data in CCP4 release: $CEXAM/toxd/toxd.mtz with columns FTOXD3 SIGFTOXD3 ANAU20 SIGANAU20 FAU20 SIGFAU20 FMM11 SIGFMM11 FI100 SIGFI100 FreeR_flag $CEXAM/tutorial/data/toxd.hkl with columns FOBS SIGMA	P2₁2₁2₁	2.2		1DTX	r1dtxsf
any from Jolly SAD, see esp. Table 1 and Table 2	see separate document on those
Calmodulin	Wilson and Brunger CCP4 test data; high resolution High resolution data inc. PDB files with ANISOU records, quite rare in PDB as yet reflection file contains _refln.intensity_meas and _refln.intensity_sigma	P1	1.0		1EXR	r1exrsf
Crambin	Jelsch et al. CCP4 test data; high resolution High resolution data inc. PDB files with ANISOU records, quite rare in PDB as yet reflection file contains _refln.F_meas_au and _refln.F_meas_sigma_au	P2₁	0.54		1EJG	r1ejgsf
GAPDH	Isupov et al. CCP4 test data; TLS asymmetric unit contains 2 monomers each of 2 domains reflection file contains _refln.F_meas_au and _refln.F_meas_sigma_au	P4₁2₁2	2.0	1b7g.tar.gz (Example TLS file)	1B7G	r1b7gsf
mannitol dehydrogenase	Hoerer et al. CCP4 test data; TLS asymmetric unit contains 3 tetramers reflection file contains _refln.F_meas and _refln.F_meas_sigma	C2	1.5	1h5q.tar.gz (Example TLS file)	1H5Q	r1h5qsf
HypF domain	Rosano et al. Hydrogenase maturation protein HypF N-terminal (acylphosphatase-like) domain (HypF-ACP) Images were collected in Hamburg on BW7A beamline with a MAR345 detector. Incident wavelenght was 0.9997 A, crystal to detector distance 250 mm, starting phi 77.0 delta phi 1.0. X beam and Y beam were (in DENZO format ...) respectively 120.010 and 119.601. Crystals belong to the H32 space group with unit cell parameters of a=b=58.5, c=156.1. Solved by SIRAS with SHARP/SOLOMON and autobuilt. However, can we use the Hg derivative data as a SAD test case? This is a nice case because there are only 84 images, total dataset size 130 Mbytes. reflection file at PDB contains _refln.F_meas and _refln.F_meas_sigma	H32	1.27	hg_images.tar (127Mb!) data for Hg derivative	1GXT	r1gxtsf
Thermolysin	Weiss et al. Thermolysin (P6122) collected at 1.9Å wavelength to 1.83Å resolution, 360 degs each. SAD case based on 1 Zn, 5 Ca, and 3 S (see Structure 9, 771-777, 2001) 315 amino acids. Autobuilt. to be included later	P6₁22	1.83
Xenon SAD	Phil Evans Lab data (CuKalpha), single xenon site, solved by SAD...I'm still working on this. to be included later
2 wavelength MAD	Ashley Deacon SSRL - is putting this together to be included later
beta:BLIP	Strynadka et al. beta-lactamase plus Beta-Lactamase Inhibitory Protein anisotropy in the data complicates molecular replacement 1jtg - BLIP from Streptomyces clavuligerus; 1jtd - BLIP-II from Streptomyces exfoliatus, both spacegroup P2₁2₁2₁	P3₂21	3.0	sfdata-betablip.tgz tar -xvzf ./sfdata-betablip.tgz to unpack into directory sfdata/ sfdata-betablip.tgz contains: betablip_beta.pdb - beta-lactamase molecular replacement model, sequence as in 1jtg and 1jtd betablip_blip.pdb - Beta-Lactamase Inhibitory Protein model, BLIP as in 1jtg beta_blip.mtz with columns Fobs Sigma	1JTG, 1JTD	r1jtgsf, r1jtdsf
Elastase (Porcine Pancreatic)	Panjikar and Tucker Br^- SAD data set Br-G1-Xe-W0.80: PPE crystals dipped in a 1:1 mixture of 1 M NaBr + 100% glycerol; subsequently pressurized under Xe; data collected at 0.8020Å reflection file at PDB contains _refln.F_meas_au and _refln.F_meas_sigma_au to be included later Other PP elastases: From the same paper: Br-oil-Xe at wavelength 0.80: 1l0z, r1l0zsf - _refln.F_meas_au and _refln.F_meas_sigma_au I SIRAS - G Sheldrick: see sfdata-elastase.tgz I SIRAS - G Evans and G Bricogne, Acta D58 (2002) 976. Solved with autoSHARP. 1gwa, r1gwasf - _refln.F_meas_au and _refln.F_meas_sigma_au. From same paper: 1c1m (Prange et al (1998) Proteins SFG 30, 61-73), which is native and Xenon/Krypton. Data: r1c1msf - _refln.F_squared_meas, _refln.F_squared_sigma, _refln.F_calc and _refln.phase_calc CaCl₂ and Na-citrate: 1lka, r1lkasf - _refln.F_meas_au, _refln.F_meas_sigma_au, _refln.ndb_anomalous_diff and _refln.ndb_anomalous_diff_sigma Na₂SO₄: 1lkb, r1lkbsf - _refln.F_meas_au, _refln.F_meas_sigma_au, _refln.ndb_anomalous_diff and _refln.ndb_anomalous_diff_sigma from Weiss et al., Acta D58 (2002) 1407. Based on 1qnj (atomic reso, Würtele et al., Acta D56 (2002) 520. Data: r1qnjsf - _refln.intensity_meas and _refln.intensity_sigma) I SAD - G Evans, M Polentarutti, K Djinovic Carugo, G Bricogne, Acta D59 (2003) 1429-1434, also using radiation damage for phasing. No refined model, so not at PDB. Xe MAD - C Mueller-Dieckmann et al., Acta D60 (2004) 28; collected at wavelengths 0.80-2.65Å, to maximum 1.65Å resolution, both in air and helium atmospheres. 1uo6, r1uo6sf - _refln.F_meas_au, _refln.F_meas_sigma_au, _refln.F_calc, _refln.phase_calc	P2₁2₁2₁	1.20	sfdata-elastase.tgz tar -xvzf ./sfdata-elastase.tgz to unpack into directory sfdata/ sfdata-elastase.tgz contains: elastase.sca - native data I/SIGI for centric and I(+)/SIGI(+)/I(-)/SIGI(-) for acentric reflections - 12 sulfurs can be found by SAD phasing from these data alone elas-nai.sca - sodium iodide soak, I/SIGI for centric and I(+)/SIGI(+)/I(-)/SIGI(-) for acentric reflections - 18 to 20 iodides can by found by SIRAS phasing using both native and iodide soak datasets; occupancy refinement is a useful tool	1l1g	r1l1gsf

Thanks a lot to everybody involved for releasing these data to the community, specifically the Autostruct partners; Zbyszek Dauter and friends for JIA and 'the Jolly SAD data'; Michael James, Natalie Strynadka and Randy Read for beta:BLIP.

Test data suggested:

molecule name	details, (potential) use	remarks
HEW lysozyme	sulphurs, high resolution, good symmetry, limited number of data	JollySAD has one lysozyme: 1lz8, r1lz8sf, sfdata-lyso.tgz (P4₃2₁2, collected at 1.54Å wavelength to 1.53Å resolution - anomalous signal of sulfurs and chlorines)
a good DNA set	would be really useful, but it would have to have standard PDB notation: *, not ' (see PDB format guide) GCTAU, not GUA CYT etc So check with REFMAC libraries and make a really good example for everyone to use.	JollySAD has one DNA: 1ICK, r1icksf, sfdata-dorota.tgz (P2₁2₁2₁, collected at 0.98Å wavelength to 0.95Å resolution - phased on phosphorus)
a protein-RNA complex
a good sugar example
different formats (mmCIF, SHELX, CSD, etc, etc)	to test conversion programs, though the problem here is keeping up-to-date with changing formats
	we don't have one specific area of interest, but rather we need a range of examples covering different spacegroups (esp. not-so-well-tested ones like H3), different levels of NCS, different resolutions, etc.
small protein	solvable by direct methods	Bence-Jones protein Rhe: 2rhe, no sf data at PDB

References:

1f8g: Buckley, P. A., Baz Jackson, J., Schneider, T., White, S. A., Rice, D. W., Baker, P. J.: Protein-Protein Recognition, Hydride Transfer and Proton Pumping in the Transhydrogenase Complex. Structure Fold Des. 8 pp. 809 (2000)
1thw: J. É. Debreczeni, G. Bunkóczi, Q. Ma, H. Blaser and G. M. Sheldrick: In-house measurement of the sulfur anomalous signal and its use for phasing, Acta Cryst. (2003). D59, 688-696
1fse: Ducros, V. M.-A., Lewis, R. J., Verma, C. S., Dodson, E. J., Leonard, G., Turkenburg, J. P., Murshudov, G. N., Wilkinson, A. J., Brannigan, J. A.: Crystal Structure of Gere, the Ultimate Transcriptional Regulator of Spore Formation in Bacillus Subtilis. J.Mol.Biol. 306 pp. 759 (2001)
1b9m: Hall, D. R., Gourley, D. G., Leonard, G. A., Duke, E. M. H., Anderson, L. A., Boxer, D. H., Hunter, W. N.: The High-Resolution Crystal Structure of the Molybdate-Dependent Transcriptional Regulator (Mode) from Escherichia Coli: A Novel Combination of Domain Folds. Embo J. 18 pp. 1435 (1999)
1h5q: Hoerer, S., Stoop, J., Mooibroek, H., Baumann, U. and Sassoon, J. J. Biol. Chem. 276, 27555 (2001)
1b7g: Isupov, M.N., Fleming, T.M., Dalby, A.R., Crowhurst, G.S., Bourne, P.C., and Littlechild, J.A. J.Mol.Biol., 291, 651 (1999)
1ejg: Jelsch, C., Teeter, M.M., Lamzin, V., Pichon-Lesme, V., Blessing, B., Lecomte, C.: Accurate protein crystallography at ultra-high resolution: valence-electron distribution in crambin. Proc.Nat.Acad.Sci.USA 97 pp. 3171 (2000)
1c8u: Li, J., Derewenda, U., Auter, Z. D., Smith, S., Derewenda, Z. S.: Crystal Structure of the Escherichia Coli Thioesterase II, a Homolog of the Human Nef-Binding Enzyme. Nat.Struct.Biol. 7 pp. 555 (2000)
1l1g: Panjikar, S. and Tucker, P.A.: Xenon derivatization of halide-soaked protein crystals. Acta Cryst. D58 (2002) 1413-1420
1gxt: Rosano C, Zuccotti S, Stefani M, Bucciantini M, Ramponi G, Bolognesi M.: Crystallization and preliminary X-ray characterization of the acylphosphatase-like domain from the Escherichia coli hydrogenase maturation factor HypF. Acta Crystallogr.,Sect.D 58 pp. 524 (2002)
1dd5: Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A., Liljas, A.: Crystal Structure of Thermotoga Maritima Ribosome Recycling Factor: A tRNA Mimic. Science 286 pp. 2349 (1999)
1lni: Sevcik, J., Lamzin, V. S., Dauter, Z., Wilson, K. S.: Atomic Resolution Data Reveal Flexibility in the Structure of Rnase Sa. Acta Crystallogr.,Sect.D 58 pp. 1307 (2002)
1dtx: Skarzynski, T.: Crystal structure of alpha-dendrotoxin from the green mamba venom and its comparison with the structure of bovine pancreatic trypsin inhibitor. J Mol Biol 224 pp. 671 (1992)
1jtg: Strynadka, N.C.J., Jensen, S.E., Alzari, P.M. & James, M.N.G. (1996). "A potent new mode of -lactamase inhibition revealed by the 1.7Å X-ray crystallographic structure of the TEM-1-BLIP complex", Nature Struct. Biol. 3, 290-297.
1dw9: Walsh, M. A., Otwinowski, Z., Perrakis, A., Anderson, P. M., Joachimiak, A.: Structure of Cyanase Reveals that a Novel Dimeric and Decameric Arrangement of Subunits is Required for Formation of the Enzyme Active Site. Structure (London) 8 pp. 505 (2000)
thermolysin: Weiss MS, Sicker T, Hilgenfeld R.: Soft X-rays, high redundancy, and proper scaling: a new procedure for automated protein structure determination via SAS. Structure (Camb) 9 pp. 771 (2001)
1exr: Wilson, M.A., Brunger, A.T.: The 1.0 Å crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J.Mol.Biol. 301 pp. 1237 (2000)

Maria Turkenburg, mgwt@ysbl.york.ac.uk