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Cytochrome c prime beta from Methylococcus capsulatus (Bath): CO complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HIH Refined from PDB 6HIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 35% PEG 550 (v/v) and 0.1 M MES, pH 6.5.
Cryoprotection in ML plus 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.8 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.49 α = 90 b = 105.49 β = 90 c = 105.49 γ = 90
Symmetry Space Group P 21 3
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 PILATUS3 6M 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.6 47.22 100 0.069 1 26.3 20 51778 25.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 2.73 0.5 1.4 20.5
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 Refined from PDB 6HIH 1.6 47.22 49120 2626 99.99 0.182 0.1811 0.1881 0.1983 0.2078 RANDOM 29.735
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 r_dihedral_angle_2_deg 31.451 r_dihedral_angle_4_deg 19.945 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 6.809 r_angle_refined_deg 2.219 r_angle_other_deg 1.503 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.451 r_dihedral_angle_4_deg 19.945 r_dihedral_angle_3_deg 11.918 r_dihedral_angle_1_deg 6.809 r_angle_refined_deg 2.219 r_angle_other_deg 1.503 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling REFMAC phasing