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Crystal structure of an oxoferryl species of catalase-peroxidase KatG at pH5.6
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 293 16-20% MPD, pH 5.6 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.15 60.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.211 α = 90 b = 114.658 β = 90 c = 174.378 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 MARRESEARCH 2005-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 1.00801 ESRF BM16
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 1.9 95.8 98.9 0.095 22.5 7.3 140763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.9 0.427 15339
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 1.9 20 140763 15522 98.78 0.1445 0.1412 0.1543 0.1749 0.1835 RANDOM 21.145
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] -0.07 0.31 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.027 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 5.978 r_mcangle_it 2.42 r_angle_refined_deg 2.183 r_mcbond_it 1.617 r_mcbond_other 1.613 r_angle_other_deg 1.164 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.027 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 13.096 r_dihedral_angle_1_deg 5.978 r_mcangle_it 2.42 r_angle_refined_deg 2.183 r_mcbond_it 1.617 r_mcbond_other 1.613 r_angle_other_deg 1.164 r_chiral_restr 0.154 r_bond_refined_d 0.026 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 11010 Nucleic Acid Atoms Solvent Atoms 1501 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALA data scaling AMoRE phasing