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Structure of the K39Q mutant of rat somatic Cytochrome c at 1.36A
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 5.5 298 Wizard Cryo 2#30: 40% PEG 600, 100mM Sodium Citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.04 40.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.578 α = 90 b = 61.153 β = 90 c = 186.065 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 EIGER X 9M 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
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 1.36 58.1 99.9 0.088 0.092 0.026 0.999 13 12.1 83554 14.69
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 1.36 1.43 99.9 0.797 0.831 0.233 0.942 2.4 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5C0Z 1.36 58.1 1.37 83395 4134 99.76 0.1431 0.1412 0.1426 0.1796 0.1803 23.6
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9971 f_angle_d 1.4665 f_chiral_restr 0.0917 f_bond_d 0.0162 f_plane_restr 0.0159
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3228 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 172
Software Software Software Name Purpose PHENIX refinement PDB-REDO refinement AutoProcess data reduction Aimless data scaling PHASER phasing