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Oxidized rat cytochrome c mutant (K53Q)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 JBS1D4: 30% PEG 2K MME, 0.1M Na MES pH 6.5, 0.1M Na Acetate
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.837 α = 90 b = 96.767 β = 90 c = 38.372 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 9M 2016-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.309 48.384 98.9 0.12 0.117 0.128 0.051 0.994 12.2 11.1 48257 12.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.309 1.332 86.8 0.821 0.806 0.887 0.325 0.896 8.6
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 5C0Z 1.31 48.38 45282 2355 98.8 0.14 0.138 0.139 0.17 0.1728 RANDOM 21.32
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 0.69 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.597 r_dihedral_angle_4_deg 21.621 r_dihedral_angle_3_deg 11.397 r_dihedral_angle_1_deg 6.547 r_long_range_B_refined 3.301 r_long_range_B_other 3.07 r_scangle_other 2.988 r_rigid_bond_restr 2.664 r_scbond_other 2.474 r_scbond_it 2.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.597 r_dihedral_angle_4_deg 21.621 r_dihedral_angle_3_deg 11.397 r_dihedral_angle_1_deg 6.547 r_long_range_B_refined 3.301 r_long_range_B_other 3.07 r_scangle_other 2.988 r_rigid_bond_restr 2.664 r_scbond_other 2.474 r_scbond_it 2.471 r_angle_refined_deg 2.276 r_mcangle_other 1.902 r_mcangle_it 1.899 r_mcbond_it 1.613 r_mcbond_other 1.571 r_angle_other_deg 1.236 r_chiral_restr 0.155 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction SCALA data scaling PHASER phasing