4RKA

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A347


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M acetate pH 4.8, 40 mM UDAO, 20.8 mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate, 1 mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4163.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.65α = 90
b = 90.65β = 90
c = 122.45γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97852SSRFBL17U

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
12.7166.0994.7162781540922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.712.86

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 REPLACEMENTTHROUGHOUT4JS32.7166.09162781540985799.690.166620.163250.2278RANDOM17.782
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]
0.040.020.04-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.403
r_dihedral_angle_4_deg18.21
r_dihedral_angle_3_deg16.077
r_dihedral_angle_1_deg6.433
r_mcangle_other2.621
r_mcangle_it2.62
r_scbond_it2.438
r_angle_refined_deg2.005
r_mcbond_it1.555
r_mcbond_other1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.403
r_dihedral_angle_4_deg18.21
r_dihedral_angle_3_deg16.077
r_dihedral_angle_1_deg6.433
r_mcangle_other2.621
r_mcangle_it2.62
r_scbond_it2.438
r_angle_refined_deg2.005
r_mcbond_it1.555
r_mcbond_other1.55
r_angle_other_deg0.876
r_chiral_restr0.086
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2792
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms99

Software

Software
Software NamePurpose
HKL-2000data collection
automodel building
REFMACrefinement
HKL-2000data reduction
iMOSFLMdata reduction
autophasing