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Crystal structure of the catalase-peroxidase from B. pseudomallei treated with hydrogen peroxide and carbon monoxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 MPD, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.21 61.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.854 α = 90 b = 113.79 β = 90 c = 174.633 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD mirrors 2015-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.88 100.854 99.5 0.09 0.102 0.046 10.7 4.4 162264 162264
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 1.88 1.98 99.7 0.57 1.3 4.6
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 1MWV 1.88 50 153938 8079 99.21 0.1786 0.1768 0.1869 0.213 0.22 RANDOM 28.029
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] -2.32 4.02 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.152 r_mcangle_it 2.989 r_angle_refined_deg 2.241 r_mcbond_it 2.053 r_mcbond_other 2.047 r_angle_other_deg 1.269 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.152 r_mcangle_it 2.989 r_angle_refined_deg 2.241 r_mcbond_it 2.053 r_mcbond_other 2.047 r_angle_other_deg 1.269 r_chiral_restr 0.157 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_gen_planes_other 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11014 Nucleic Acid Atoms Solvent Atoms 1415 Heterogen Atoms 134
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing