9EZS | pdb_00009ezs

XFEL structure of free hNQO1 unmixed (P4502)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2980.1 M Tris pH 8.5, 0.2 M sodium acetate, 25% polyethylene glycol (PEG) 3350
Crystal Properties
Matthews coefficientSolvent content
2.6152.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.5α = 90
b = 107.8β = 90
c = 198.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELAGIPD2022-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASEREUROPEAN XFEL BEAMLINE SPB/SFX1.7712European 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
12.326.711000.2253.523756465
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)
12.32.361.268

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 REPLACEMENTTHROUGHOUT2.526.7144142233999.870.180150.177550.18510.229110.1843RANDOM39.046
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]
0.360.27-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.601
r_long_range_B_refined10.382
r_long_range_B_other10.295
r_dihedral_angle_2_deg7.355
r_scangle_other7.207
r_dihedral_angle_1_deg6.457
r_mcangle_other5.566
r_mcangle_it5.564
r_scbond_it4.398
r_scbond_other4.397
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.601
r_long_range_B_refined10.382
r_long_range_B_other10.295
r_dihedral_angle_2_deg7.355
r_scangle_other7.207
r_dihedral_angle_1_deg6.457
r_mcangle_other5.566
r_mcangle_it5.564
r_scbond_it4.398
r_scbond_other4.397
r_mcbond_it3.571
r_mcbond_other3.57
r_angle_refined_deg1.497
r_angle_other_deg0.512
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.006
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 Atoms8915
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing