☰ Navigation Tabs
SSX structure of cytochrome c prime beta from Methylococcus capsulatus (Bath)
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 2.96 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.227 α = 90 b = 107.227 β = 90 c = 107.227 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 EIGER2 X CdTe 9M 2023-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.620 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 2.15 75.82 100 0.984 0.188 12.9 69.9 22647
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 2.15 2.19 100 0.279 1.017 58.1
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 2.151 61.984 22641 1097 99.996 0.198 0.1962 0.1962 0.2371 0.2369 39.596
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 13.856 r_dihedral_angle_3_deg 13.484 r_lrange_it 9.014 r_dihedral_angle_1_deg 7.623 r_scangle_it 6.133 r_dihedral_angle_2_deg 5.535 r_mcangle_it 4.147 r_scbond_it 3.905 r_mcbond_it 2.867 r_angle_refined_deg 1.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.856 r_dihedral_angle_3_deg 13.484 r_lrange_it 9.014 r_dihedral_angle_1_deg 7.623 r_scangle_it 6.133 r_dihedral_angle_2_deg 5.535 r_mcangle_it 4.147 r_scbond_it 3.905 r_mcbond_it 2.867 r_angle_refined_deg 1.667 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.303 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.086 r_metal_ion_refined 0.026 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2133 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing Coot model building