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Cytochrome c prime beta from Methylococcus capsulatus (Bath) in complex with nitric oxide from proli NONOate
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 291 Final concentrations: 20 mg/mL protein, 50 mM HEPES pH 7.5, 34 % (v/v) polyethylene glycol 550, 500 mM MES pH 6.5, 5 mM ZnSO4.
Crystal Properties Matthews coefficient Solvent content 2.97 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.441 α = 90 b = 107.441 β = 90 c = 107.441 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 293 PIXEL DECTRIS PILATUS3 6M 2019-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Oxford silicon chip Geobrick and Smaract
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.85 76.09 100 0.998 0.068 11 175.4 35508
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.534 0.936 0.9 137.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 76.088 35507 1729 100 0.156 0.1551 0.1551 0.1795 0.1796 34.669
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_6_deg 15.336 r_dihedral_angle_3_deg 13.068 r_lrange_it 9.82 r_scangle_it 8.392 r_dihedral_angle_1_deg 7.056 r_dihedral_angle_2_deg 6.589 r_scbond_it 5.663 r_mcangle_it 5.039 r_mcbond_it 3.682 r_angle_refined_deg 2.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.336 r_dihedral_angle_3_deg 13.068 r_lrange_it 9.82 r_scangle_it 8.392 r_dihedral_angle_1_deg 7.056 r_dihedral_angle_2_deg 6.589 r_scbond_it 5.663 r_mcangle_it 5.039 r_mcbond_it 3.682 r_angle_refined_deg 2.553 r_nbtor_refined 0.316 r_metal_ion_refined 0.245 r_symmetry_nbd_refined 0.212 r_nbd_refined 0.208 r_chiral_restr 0.147 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 104
Software Software Software Name Purpose DIALS data reduction xia2 data reduction MOLREP phasing Coot model building REFMAC refinement xia2 data scaling