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The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
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 6.5 295 20 mg/ml protein, PEG 4000, isopropanol, sodium acetate, potassium ferricyanate
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.517 α = 109.86 b = 52.567 β = 92.93 c = 61.771 γ = 92.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2014-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.362 57.962 92.37 0.052 14.1 3.9 80448 76544 13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.362 1.398 66.24 0.58 2.2 3.8
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 1.362 57.96 76544 3901 92.37 0.131 0.129 0.1291 0.16982 0.1682 RANDOM 21.413
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] 0.04 0.04 0.89 -0.51 0.85 -0.22
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.915 r_dihedral_angle_2_deg 31.917 r_dihedral_angle_4_deg 31.575 r_sphericity_bonded 12.158 r_dihedral_angle_3_deg 12.075 r_dihedral_angle_1_deg 6.497 r_long_range_B_refined 3.725 r_long_range_B_other 3.046 r_rigid_bond_restr 2.519 r_scangle_other 2.45
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.915 r_dihedral_angle_2_deg 31.917 r_dihedral_angle_4_deg 31.575 r_sphericity_bonded 12.158 r_dihedral_angle_3_deg 12.075 r_dihedral_angle_1_deg 6.497 r_long_range_B_refined 3.725 r_long_range_B_other 3.046 r_rigid_bond_restr 2.519 r_scangle_other 2.45 r_scbond_it 2.042 r_scbond_other 2.033 r_mcangle_it 1.824 r_mcangle_other 1.824 r_angle_refined_deg 1.803 r_mcbond_it 1.482 r_mcbond_other 1.482 r_angle_other_deg 1.058 r_chiral_restr 0.122 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.014 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3220 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement PHENIX phasing Aimless data scaling XDS data reduction