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XFEL structure of the free hNQO1 unmixed (P3083)
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 7.5 298 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.6 α = 90 b = 107.7 β = 90 c = 198.6 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 298 PIXEL AGIPD 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.3332 European XFEL SPB/SFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
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 27.03 100 0.204 4.3 489 44040
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 0.695
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 27.03 44040 2350 99.39 0.19419 0.19205 0.2 0.23483 0.2401 RANDOM 46.879
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 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.88 r_long_range_B_other 10.274 r_long_range_B_refined 10.272 r_scangle_other 7.829 r_dihedral_angle_1_deg 6.486 r_dihedral_angle_2_deg 6.169 r_mcangle_other 5.821 r_mcangle_it 5.818 r_scbond_it 4.786 r_scbond_other 4.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.88 r_long_range_B_other 10.274 r_long_range_B_refined 10.272 r_scangle_other 7.829 r_dihedral_angle_1_deg 6.486 r_dihedral_angle_2_deg 6.169 r_mcangle_other 5.821 r_mcangle_it 5.818 r_scbond_it 4.786 r_scbond_other 4.779 r_mcbond_it 3.74 r_mcbond_other 3.732 r_angle_refined_deg 1.376 r_angle_other_deg 0.478 r_chiral_restr 0.067 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 8891 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing