9EZR | pdb_00009ezr

XFEL structure of hNQO1 mixed with NADH in an extended orientation at 0.3 s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9EZQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE8.52980.1 M Tris pH 8.5, 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties
Matthews coefficientSolvent content
2.5952.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.6α = 90
b = 107.7β = 90
c = 198.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELAGIPD2021-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASEREUROPEAN XFEL BEAMLINE SPB/SFX1.3332European XFELSPB/SFX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.525.641000.223.728742064
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.512.571001.271204

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5125.6442064217695.820.199950.197180.2090.25490.2608RANDOM57.11
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]
0.090.02-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other19.249
r_long_range_B_refined19.143
r_dihedral_angle_3_deg14.865
r_scangle_other9.397
r_dihedral_angle_2_deg7.708
r_dihedral_angle_1_deg6.415
r_mcangle_other6.364
r_mcangle_it6.362
r_scbond_it5.562
r_scbond_other5.561
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other19.249
r_long_range_B_refined19.143
r_dihedral_angle_3_deg14.865
r_scangle_other9.397
r_dihedral_angle_2_deg7.708
r_dihedral_angle_1_deg6.415
r_mcangle_other6.364
r_mcangle_it6.362
r_scbond_it5.562
r_scbond_other5.561
r_mcbond_it3.973
r_mcbond_other3.963
r_angle_refined_deg1.345
r_angle_other_deg0.458
r_chiral_restr0.062
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms8991
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing