6GK0

HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH CLASS III HISTONE DEACETYLASE INHIBITOR


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.829330% glycerol, 100 mM sodium acetate pH 4.8, 1.8 M Ammoniumsulphate, 40 mM DDAO, 6.4 mM C11DAO, 2 mM L-DHO, 1 mM Tenovin
Crystal Properties
Matthews coefficientSolvent content
3.6466.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.524α = 90
b = 90.524β = 90
c = 122.806γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.000MAX III911-3

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
11.852099.85.44.550141
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.89

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.8519.8147568254099.660.169270.168010.19301RANDOM29.791
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]
0.410.210.41-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.733
r_dihedral_angle_4_deg18.525
r_dihedral_angle_3_deg14.996
r_long_range_B_refined7.677
r_long_range_B_other7.676
r_dihedral_angle_1_deg6.816
r_scangle_other4.447
r_scbond_it2.806
r_scbond_other2.805
r_mcangle_it2.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.733
r_dihedral_angle_4_deg18.525
r_dihedral_angle_3_deg14.996
r_long_range_B_refined7.677
r_long_range_B_other7.676
r_dihedral_angle_1_deg6.816
r_scangle_other4.447
r_scbond_it2.806
r_scbond_other2.805
r_mcangle_it2.471
r_mcangle_other2.458
r_angle_refined_deg2.015
r_mcbond_it1.559
r_mcbond_other1.519
r_angle_other_deg1.083
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.006
r_bond_other_d0.001
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 Atoms2773
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing