2PRH

The structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82980.1M acetate, 1.6-2.4M ammonium sulphate, 30% glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6466.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.55α = 90
b = 90.55β = 90
c = 122.7γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2004-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.092MAX III711

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.320750.1180.12125.229077290772121.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.34940.4170.3094.615.183134

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1D3G2.419.362231972319511601000.220.1740.1720.217RANDOM15.627
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]
0.30.150.3-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.1
r_dihedral_angle_4_deg18.417
r_dihedral_angle_3_deg14.443
r_dihedral_angle_1_deg5.768
r_scangle_it2.359
r_scbond_it1.416
r_angle_refined_deg1.263
r_mcangle_it0.808
r_mcbond_it0.496
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.1
r_dihedral_angle_4_deg18.417
r_dihedral_angle_3_deg14.443
r_dihedral_angle_1_deg5.768
r_scangle_it2.359
r_scbond_it1.416
r_angle_refined_deg1.263
r_mcangle_it0.808
r_mcbond_it0.496
r_nbtor_refined0.297
r_nbd_refined0.213
r_symmetry_vdw_refined0.213
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.091
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2727
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing