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XFEL structure of free hNQO1 unmixed (P4502)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished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 298 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
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 2.3 26.71 100 0.225 3.5 237 56465
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 2.3 2.36 1.268
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 26.71 44142 2339 99.87 0.18015 0.17755 0.1851 0.22911 0.1843 RANDOM 39.046
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] 0.36 0.27 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.601 r_long_range_B_refined 10.382 r_long_range_B_other 10.295 r_dihedral_angle_2_deg 7.355 r_scangle_other 7.207 r_dihedral_angle_1_deg 6.457 r_mcangle_other 5.566 r_mcangle_it 5.564 r_scbond_it 4.398 r_scbond_other 4.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.601 r_long_range_B_refined 10.382 r_long_range_B_other 10.295 r_dihedral_angle_2_deg 7.355 r_scangle_other 7.207 r_dihedral_angle_1_deg 6.457 r_mcangle_other 5.566 r_mcangle_it 5.564 r_scbond_it 4.398 r_scbond_other 4.397 r_mcbond_it 3.571 r_mcbond_other 3.57 r_angle_refined_deg 1.497 r_angle_other_deg 0.512 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 8915 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing