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X-ray structure of bovine heart cytochrome c at high ionic strength
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 3.2-3.4 M ammonium sulfate and 0.4-0.5 M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.35 α = 90 b = 83.35 β = 90 c = 92.49 γ = 120
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 165 mm 2017-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.966 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.74 56.9 99.6 0.04 0.999 20.4 6 12830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.78 100 0.8 0.725
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 2B4Z 1.74 56.9 12192 638 99.53 0.16289 0.16072 0.1696 0.20255 0.2157 RANDOM 36.657
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] -0.31 -0.15 -0.31 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 34.581 r_dihedral_angle_3_deg 15.816 r_long_range_B_refined 8.327 r_long_range_B_other 8.247 r_scangle_other 7.346 r_dihedral_angle_1_deg 6.333 r_scbond_it 4.901 r_scbond_other 4.864 r_mcangle_other 3.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 34.581 r_dihedral_angle_3_deg 15.816 r_long_range_B_refined 8.327 r_long_range_B_other 8.247 r_scangle_other 7.346 r_dihedral_angle_1_deg 6.333 r_scbond_it 4.901 r_scbond_other 4.864 r_mcangle_other 3.782 r_mcangle_it 3.768 r_mcbond_it 2.901 r_mcbond_other 2.83 r_angle_refined_deg 2.075 r_angle_other_deg 1.118 r_chiral_restr 0.124 r_bond_refined_d 0.022 r_gen_planes_refined 0.017 r_gen_planes_other 0.013 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 814 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing