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Crystal structure of the W202F variant of catalase-peroxidase from B. pseudomallei with INH bound.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MWV PDBID 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 3.23 61.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.531 α = 90 b = 114.896 β = 90 c = 174.099 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 2017-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.98 CLSI 08B1-1
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 1.92 174.099 88.8 0.078 0.093 0.048 9.4 3.3 136130 136130
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.02 97.3 0.516 0.516 0.618 0.331 1.5 3.2
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 PDBID 1MWV 1.92 174.099 129234 6845 88.4 0.1676 0.1659 0.1772 0.1989 0.2064 RANDOM 26.538
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] -0.59 1.62 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.544 r_dihedral_angle_4_deg 17.749 r_dihedral_angle_3_deg 14.022 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.399 r_angle_other_deg 0.764 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.544 r_dihedral_angle_4_deg 17.749 r_dihedral_angle_3_deg 14.022 r_dihedral_angle_1_deg 6.708 r_angle_refined_deg 1.399 r_angle_other_deg 0.764 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11004 Nucleic Acid Atoms Solvent Atoms 1272 Heterogen Atoms 152
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing