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Helicobacter pylori strain SS1 KatA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M sodium acetate, pH 4.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.512 α = 90 b = 96.198 β = 90 c = 154.754 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.87 55.3 100 0.99 8.45 12.94 84023 15.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.94 100 0.57 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.87 55.3 1.34 84015 2000 99.99 0.143 0.1418 0.1414 0.191 0.191 18.26
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.4361 f_angle_d 0.9987 f_chiral_restr 0.0582 f_plane_restr 0.0117 f_bond_d 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8013 Nucleic Acid Atoms Solvent Atoms 1191 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement Coot model building Aimless data scaling DIALS data reduction PHASER phasing