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The crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a His175Me-His proximal ligand substitution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 5 mM cobalt(II) chloride hexahydrate, 5 mM cadmium chloride hemi(pentahydrate), 5 mM magnesium chloride hexahydrate, 5 mM nickel(II) chloride hexahydrate, 0.1 M HEPES pH 7.5 and 12% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.92 α = 90 b = 106.77 β = 90 c = 163.72 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 PIXEL DECTRIS PILATUS 6M-F 2018-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9159 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 81.86 99.11 0.052 0.057 0.022 0.999 19.2 6.6 100412 33.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 97.15 0.392 0.425 0.163 0.966 4.3 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.9 81.86 95376 4974 99.05 0.1796 0.1783 0.1917 0.2054 0.2177 RANDOM 33.345
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] 4.54 -3.44 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.743 r_dihedral_angle_4_deg 23.708 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 5.697 r_angle_refined_deg 1.222 r_angle_other_deg 0.919 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.743 r_dihedral_angle_4_deg 23.708 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 5.697 r_angle_refined_deg 1.222 r_angle_other_deg 0.919 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7222 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing