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Crystal structure of the Q233E/N240D variant of the catalase-peroxidase from B. pseudomallei
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 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.723 α = 90 b = 115.053 β = 90 c = 174.512 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 0.97949 CLSI 08ID-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 1.75 96.06 98.4 0.062 12.8 2.7 199866
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 1.75 1.84 99.2 0.413 1.7 2.7
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 1.75 96.06 189792 10034 98.03 0.1537 0.1523 0.1645 0.1817 0.1915 RANDOM 20.742
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] -0.45 1.69 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.989 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 6.101 r_mcangle_it 2.485 r_angle_refined_deg 2.226 r_mcbond_it 1.624 r_mcbond_other 1.624 r_angle_other_deg 1.265 r_chiral_restr 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.989 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 13.342 r_dihedral_angle_1_deg 6.101 r_mcangle_it 2.485 r_angle_refined_deg 2.226 r_mcbond_it 1.624 r_mcbond_other 1.624 r_angle_other_deg 1.265 r_chiral_restr 0.155 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_gen_planes_other 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11012 Nucleic Acid Atoms Solvent Atoms 1629 Heterogen Atoms 126
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction