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Crystal structure of Helicobacter pylori catalase compound I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QWL PDB entry 1QWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 15% PEG MME550, 0.1M Sodium citrate, 10mM ZnSO4, 3mM Sodium azide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.385 α = 90 b = 154.286 β = 90 c = 95.808 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 4 2003-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.97950 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.86 37 97.4 0.084 6.4 4.1 80997 74135 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.86 1.95 97.4 0.4 1.5 3.7 11375
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1QWL 1.86 37 74135 3928 96.4 0.15051 0.14847 0.1564 0.18845 0.1935 RANDOM 13.633
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] 0.64 -0.32 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.846 r_dihedral_angle_4_deg 18.539 r_dihedral_angle_3_deg 14.184 r_dihedral_angle_1_deg 6.302 r_scangle_it 2.625 r_scbond_it 1.931 r_angle_refined_deg 1.555 r_angle_other_deg 1.394 r_mcangle_it 1.153 r_mcbond_it 1.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.846 r_dihedral_angle_4_deg 18.539 r_dihedral_angle_3_deg 14.184 r_dihedral_angle_1_deg 6.302 r_scangle_it 2.625 r_scbond_it 1.931 r_angle_refined_deg 1.555 r_angle_other_deg 1.394 r_mcangle_it 1.153 r_mcbond_it 1.007 r_symmetry_vdw_other 0.251 r_mcbond_other 0.209 r_nbd_refined 0.206 r_nbd_other 0.203 r_symmetry_hbond_refined 0.19 r_symmetry_vdw_refined 0.186 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.108 r_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8135 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing