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McCP in complex with photocaged nitric oxide, 1.44 s, 1600 microjoule, SSX
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 = 107.441 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 Oxford silicon chip fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 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 1.8 76.09 100 0.986 0.07 10.2 159.8 38525
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 1.8 1.83 100 0.291 1.234 0.7 127.2
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 76.09 38523 2038 100 0.162 0.1605 0.1648 0.1946 0.1986 35.534
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 15.525 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 10.561 r_lrange_it 10.187 r_scangle_it 8.971 r_scbond_it 5.953 r_dihedral_angle_2_deg 5.645 r_mcangle_it 4.6 r_mcbond_it 3.53 r_angle_refined_deg 2.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.525 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 10.561 r_lrange_it 10.187 r_scangle_it 8.971 r_scbond_it 5.953 r_dihedral_angle_2_deg 5.645 r_mcangle_it 4.6 r_mcbond_it 3.53 r_angle_refined_deg 2.514 r_nbtor_refined 0.313 r_metal_ion_refined 0.28 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.176 r_chiral_restr 0.131 r_xyhbond_nbd_refined 0.108 r_symmetry_xyhbond_nbd_refined 0.06 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 104
Software Software Software Name Purpose DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing REFMAC refinement Coot model building