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Crystal structure of human NQO1 by serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXQ
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, 20 um FAD
Crystal Properties Matthews coefficient Solvent content 2.65 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.4 α = 90 b = 107.6 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 SLAC ePix10k 2021-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.2848 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Modular Droplet Injector injection
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 Modular Droplet Injector 5 (µl/min) undefined (µm) Crystals in mother liquor encapsulated into oil droplets
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.7 24 100 0.9668 1.9 46 36928
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 2.7 2.8 100 0.458
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DXQ 2.7 23.922 36835 1822 99.724 0.227 0.225 0.2286 0.2687 0.2712 0.1 45.992
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] 0.363 0.054 -0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.632 r_dihedral_angle_6_deg 14.859 r_dihedral_angle_2_deg 8.131 r_lrange_it 7.232 r_lrange_other 7.232 r_dihedral_angle_1_deg 6.698 r_scangle_it 4.699 r_scangle_other 4.699 r_mcangle_it 4.172 r_mcangle_other 4.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.632 r_dihedral_angle_6_deg 14.859 r_dihedral_angle_2_deg 8.131 r_lrange_it 7.232 r_lrange_other 7.232 r_dihedral_angle_1_deg 6.698 r_scangle_it 4.699 r_scangle_other 4.699 r_mcangle_it 4.172 r_mcangle_other 4.172 r_scbond_it 2.714 r_scbond_other 2.714 r_mcbond_it 2.491 r_mcbond_other 2.49 r_angle_refined_deg 1.162 r_angle_other_deg 0.381 r_dihedral_angle_other_2_deg 0.324 r_symmetry_nbd_refined 0.279 r_nbd_other 0.274 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.211 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.184 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.05 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8646 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction Aimless data scaling PHASER phasing