4QOD

The value crystal structure of apo quinone reductase 2 at 1.35A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QWXpdb entry 2QWX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.1M HEPES pH7, 1.4M AmSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.12α = 90
b = 83.2β = 90
c = 106.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELPSI PILATUS 6M2014-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9785SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.3549.6599.62104457104457
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4398.61.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2QWX1.3549.65109957104457549899.620.152680.150660.19112RANDOM25.535
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]
0.36-0.04-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.506
r_dihedral_angle_2_deg35.071
r_dihedral_angle_4_deg17.946
r_sphericity_bonded17.181
r_dihedral_angle_3_deg12.327
r_long_range_B_refined7.231
r_long_range_B_other6.978
r_scangle_other6.78
r_rigid_bond_restr6.704
r_dihedral_angle_1_deg6.481
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free41.506
r_dihedral_angle_2_deg35.071
r_dihedral_angle_4_deg17.946
r_sphericity_bonded17.181
r_dihedral_angle_3_deg12.327
r_long_range_B_refined7.231
r_long_range_B_other6.978
r_scangle_other6.78
r_rigid_bond_restr6.704
r_dihedral_angle_1_deg6.481
r_scbond_other5.785
r_scbond_it5.784
r_mcangle_it4.109
r_mcangle_other4.108
r_mcbond_it3.993
r_mcbond_other3.974
r_angle_refined_deg2.181
r_angle_other_deg1.033
r_chiral_restr0.134
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3626
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms38

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction