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SFX 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 2.95 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.1 α = 90 b = 107.1 β = 90 c = 107.1 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 300 CCD MPCCD 2019-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.127 SACLA BL2
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 chips Geobrick and Smaract
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 2.56 11 (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 1.8 33.89 100 0.938 0.204 4 233.7 38160
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 1.9 1.93 100 0.639 0.492 2.1 159.9
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 1.8 33.89 38147 1886 99.945 0.191 0.19 0.19 0.219 0.2191 29.718
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 16.031 r_dihedral_angle_3_deg 12.124 r_lrange_it 7.434 r_lrange_other 7.401 r_dihedral_angle_1_deg 6.846 r_dihedral_angle_2_deg 6.572 r_scangle_it 4.825 r_scangle_other 4.823 r_scbond_other 3.124 r_scbond_it 3.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.031 r_dihedral_angle_3_deg 12.124 r_lrange_it 7.434 r_lrange_other 7.401 r_dihedral_angle_1_deg 6.846 r_dihedral_angle_2_deg 6.572 r_scangle_it 4.825 r_scangle_other 4.823 r_scbond_other 3.124 r_scbond_it 3.123 r_angle_refined_deg 2.317 r_mcangle_other 2.309 r_mcangle_it 2.307 r_mcbond_it 1.611 r_mcbond_other 1.611 r_angle_other_deg 0.628 r_nbd_refined 0.204 r_symmetry_nbd_other 0.201 r_nbd_other 0.195 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.124 r_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_other 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2126 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 105
Software Software Software Name Purpose CrystFEL data reduction PRIME data scaling MOLREP phasing REFMAC refinement Coot model building