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Oxidized rat cytochrome c mutant (S47E)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C0Z 5c0z.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 JBS7D5: 47% MPD, 2% tert Butanol
Crystal Properties Matthews coefficient Solvent content 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.705 α = 109.89 b = 52.357 β = 92.66 c = 61.819 γ = 91.15
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 MAR CCD 130 mm 2014-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.55 58.04 96.4 0.056 0.074 0.048 0.995 7.2 2.2 56969 15.2
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 1.55 1.7 94.9 0.296 0.398 0.263 0.862 2.1
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.pdb 1.55 58.04 54088 2880 96.41 0.1675 0.1661 0.1757 0.1924 0.1975 RANDOM 24.392
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] 0.91 -1.74 -0.42 0.22 -0.46 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 34.193 r_dihedral_angle_2_deg 30.289 r_dihedral_angle_3_deg 12.853 r_dihedral_angle_1_deg 7.032 r_angle_refined_deg 2.344 r_angle_other_deg 1.441 r_chiral_restr 0.132 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 34.193 r_dihedral_angle_2_deg 30.289 r_dihedral_angle_3_deg 12.853 r_dihedral_angle_1_deg 7.032 r_angle_refined_deg 2.344 r_angle_other_deg 1.441 r_chiral_restr 0.132 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3240 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 232
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction