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Crystal structure of the L326D 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 MPD, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.24 62.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.793 α = 90 b = 115.227 β = 90 c = 174.543 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) 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 1.87 96.162 98.9 0.092 0.105 0.05 9.3 4.1 165881 165881
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 1.87 1.97 99.8 0.478 1.6 4.2
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 1MWV 1.87 48.419 157637 8160 98.82 0.1654 0.1637 0.1738 0.1979 0.2072 RANDOM 27.851
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] -0.95 1.94 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.274 r_mcangle_it 3.004 r_angle_refined_deg 2.319 r_mcbond_it 2.095 r_mcbond_other 2.092 r_angle_other_deg 1.194 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.515 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.274 r_mcangle_it 3.004 r_angle_refined_deg 2.319 r_mcbond_it 2.095 r_mcbond_other 2.092 r_angle_other_deg 1.194 r_chiral_restr 0.156 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_gen_planes_other 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11030 Nucleic Acid Atoms Solvent Atoms 1271 Heterogen Atoms 136
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction