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McCP in complex with photocaged nitric oxide, 1.44 s, 0.95 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 2.97 63.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.408 α = 90 b = 107.408 β = 90 c = 107.408 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 2021-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.00 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 1.8 76.064 100 0.993 0.111 6.3 59.7 38471
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 0.399 0.943 0.7 47.1
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 1.8 76.064 38471 1997 100 0.162 0.1613 0.1651 0.1815 0.1851 31.963
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 14.427 r_dihedral_angle_3_deg 13.028 r_lrange_it 9.735 r_scangle_it 8.722 r_dihedral_angle_2_deg 6.748 r_dihedral_angle_1_deg 6.412 r_scbond_it 5.699 r_mcangle_it 4.603 r_mcbond_it 3.359 r_angle_refined_deg 2.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.427 r_dihedral_angle_3_deg 13.028 r_lrange_it 9.735 r_scangle_it 8.722 r_dihedral_angle_2_deg 6.748 r_dihedral_angle_1_deg 6.412 r_scbond_it 5.699 r_mcangle_it 4.603 r_mcbond_it 3.359 r_angle_refined_deg 2.203 r_nbtor_refined 0.318 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.207 r_chiral_restr 0.146 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement DIALS data reduction PRIME data scaling MOLREP phasing Coot model building