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The crystal structure of Helicobacter pylori L-asparaginase at 1.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WSA PDB ENTRY 1WSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN WAS CRYSTALLIZED FROM 17.5% W/V PEG 4000, 0.1 M MG FORMATE, 0.1 M HEPES-NAOH, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.559 α = 90 b = 94.796 β = 90 c = 100.342 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH SX-165 2007-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 20 99.7 0.1 22.8 7.1 59013 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 99.1 0.27 7.2 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 1WSA 1.4 20 58995 2939 99.5 0.1264 0.1312 0.1264 0.1687 0.1231 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2780.35
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.796 s_anti_bump_dis_restr 0.41 s_approx_iso_adps 0.094 s_zero_chiral_vol 0.066 s_similar_adp_cmpnt 0.055 s_angle_d 0.032 s_from_restr_planes 0.0307 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2448 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 9
Software Software Software Name Purpose SHELXL-97 refinement HKL data reduction HKL data scaling PHASER phasing