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Crystal structure of the S324G variant of 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 16-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.909 α = 90 b = 113.894 β = 90 c = 174.789 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 0.97944 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 1.85 95.423 98.8 0.064 13.2 3.6 168868
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 1.85 1.95 99.9 0.506 1.5 3.5
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 1.85 20 160442 8324 98.29 0.1525 0.1507 0.1618 0.1874 0.1947 RANDOM 26.459
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] -0.79 2.52 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 13.855 r_dihedral_angle_1_deg 6.014 r_mcangle_it 2.928 r_angle_refined_deg 2.275 r_mcbond_it 2.112 r_mcbond_other 2.102 r_angle_other_deg 1.209 r_chiral_restr 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 13.855 r_dihedral_angle_1_deg 6.014 r_mcangle_it 2.928 r_angle_refined_deg 2.275 r_mcbond_it 2.112 r_mcbond_other 2.102 r_angle_other_deg 1.209 r_chiral_restr 0.167 r_bond_refined_d 0.029 r_gen_planes_refined 0.016 r_gen_planes_other 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11010 Nucleic Acid Atoms Solvent Atoms 1390 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data scaling SCALA data scaling MOLREP phasing