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McCP in complex with photocaged nitric oxide, 20 ms, 12.9 microjoule, SFX
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 = 107.766 α = 90 b = 107.766 β = 90 c = 107.766 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 2022-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.25 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 SACLA HVE injector injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 2.6 9.94 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 SACLA HVE injector undefined (µl/min) undefined (µm)
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 2.25 29.907 100 0.996 0.109 6.3 430.4 20088
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 2.25 2.29 100 0.358 1.16 0.6
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 2.25 29.907 20083 1080 99.94 0.192 0.1902 0.1937 0.2228 0.2254 50.194
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_3_deg 13.743 r_dihedral_angle_6_deg 13.584 r_lrange_it 10.757 r_scangle_it 9.293 r_dihedral_angle_1_deg 7.453 r_dihedral_angle_2_deg 6.848 r_scbond_it 6.231 r_mcangle_it 5.673 r_mcbond_it 4.056 r_angle_refined_deg 1.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.743 r_dihedral_angle_6_deg 13.584 r_lrange_it 10.757 r_scangle_it 9.293 r_dihedral_angle_1_deg 7.453 r_dihedral_angle_2_deg 6.848 r_scbond_it 6.231 r_mcangle_it 5.673 r_mcbond_it 4.056 r_angle_refined_deg 1.927 r_nbtor_refined 0.313 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.168 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 97
Software Software Software Name Purpose DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing Coot model building REFMAC refinement