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Human NOQ1 enzyme in its holo form by serial crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 293 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62 α = 90 b = 108 β = 90 c = 200 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL PSI JUNGFRAU 4M 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
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 Small SOS chips
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 100 97.1 0.142 9.9 154.1 41455
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 1.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 100 41455 4581 97.12 0.20281 0.19873 0.2101 0.23869 0.245 RANDOM 69.291
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] 0.01 0.08 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_long_range_B_refined 10.18 r_long_range_B_other 10.179 r_mcangle_it 8.428 r_mcangle_other 8.427 r_scangle_other 7.724 r_dihedral_angle_1_deg 6.522 r_dihedral_angle_2_deg 5.995 r_mcbond_it 5.482 r_mcbond_other 5.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.84 r_long_range_B_refined 10.18 r_long_range_B_other 10.179 r_mcangle_it 8.428 r_mcangle_other 8.427 r_scangle_other 7.724 r_dihedral_angle_1_deg 6.522 r_dihedral_angle_2_deg 5.995 r_mcbond_it 5.482 r_mcbond_other 5.481 r_scbond_it 4.95 r_scbond_other 4.936 r_angle_refined_deg 1.372 r_angle_other_deg 0.462 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8882 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing