4IGH

High resolution crystal structure of human dihydroorotate dehydrogenase bound with 4-quinoline carboxylic acid analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D3GPDB ENTRY 1D3G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42961.72 M ammonium sulfate, 0.1 M sodium acetate, pH 5.4, 1.5 M sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.665.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.786α = 90
b = 90.786β = 90
c = 122.485γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.2278.6299.660.066277.11724071718292211.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.221.241000.937278552

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1D3G1.378.6222172407171829430499.530.137910.137610.14764RANDOM
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]
0.230.120.23-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free77.794
r_dihedral_angle_2_deg36.482
r_sphericity_bonded18.107
r_dihedral_angle_4_deg17.627
r_dihedral_angle_3_deg13.008
r_rigid_bond_restr10.162
r_dihedral_angle_1_deg6.462
r_angle_refined_deg2.583
r_angle_other_deg1.394
r_chiral_restr0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free77.794
r_dihedral_angle_2_deg36.482
r_sphericity_bonded18.107
r_dihedral_angle_4_deg17.627
r_dihedral_angle_3_deg13.008
r_rigid_bond_restr10.162
r_dihedral_angle_1_deg6.462
r_angle_refined_deg2.583
r_angle_other_deg1.394
r_chiral_restr0.233
r_bond_refined_d0.027
r_gen_planes_refined0.016
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2719
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms105

Software

Software
Software NamePurpose
HKL-3000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling