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McCP in complex with photocaged nitric oxide, dark control, 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 = 107.314 α = 90 b = 107.314 β = 90 c = 107.314 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 2.2 75.998 100 0.974 0.184 9 40 21205
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 2.2 2.24 0.373 0.753 1.9
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 2.2 75.998 21194 1071 100 0.194 0.1922 0.1922 0.2307 0.231 41.162
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 13.912 r_dihedral_angle_6_deg 12.585 r_lrange_it 8.228 r_dihedral_angle_1_deg 7.054 r_scangle_it 6.555 r_dihedral_angle_2_deg 5.698 r_scbond_it 4.121 r_mcangle_it 3.838 r_mcbond_it 2.49 r_angle_refined_deg 2.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.912 r_dihedral_angle_6_deg 12.585 r_lrange_it 8.228 r_dihedral_angle_1_deg 7.054 r_scangle_it 6.555 r_dihedral_angle_2_deg 5.698 r_scbond_it 4.121 r_mcangle_it 3.838 r_mcbond_it 2.49 r_angle_refined_deg 2.112 r_symmetry_nbd_refined 0.373 r_nbtor_refined 0.309 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.112 r_symmetry_xyhbond_nbd_refined 0.096 r_gen_planes_refined 0.009 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2146 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 94
Software Software Software Name Purpose DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing REFMAC refinement Coot model building