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XFEL structure of hNQO1 mixed with NADH for 1.2 s
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 298 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.5 α = 90 b = 107.8 β = 90 c = 198.1 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 2022-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.7712 European XFEL SPB/SFX
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 26.47 98.35 0.285 2.8 115 43444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 0.5464
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 26.47 43444 2326 98.35 0.19467 0.19181 0.1991 0.25009 0.252 RANDOM 52.512
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] 0.08 0.05 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.649 r_long_range_B_refined 13.391 r_long_range_B_other 13.304 r_scangle_other 8.059 r_dihedral_angle_1_deg 6.548 r_dihedral_angle_2_deg 6.475 r_mcangle_other 6.135 r_mcangle_it 6.132 r_scbond_it 4.85 r_scbond_other 4.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.649 r_long_range_B_refined 13.391 r_long_range_B_other 13.304 r_scangle_other 8.059 r_dihedral_angle_1_deg 6.548 r_dihedral_angle_2_deg 6.475 r_mcangle_other 6.135 r_mcangle_it 6.132 r_scbond_it 4.85 r_scbond_other 4.849 r_mcbond_it 3.885 r_mcbond_other 3.879 r_angle_refined_deg 1.308 r_angle_other_deg 0.458 r_chiral_restr 0.06 r_bond_refined_d 0.005 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 8972 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing