3MJY

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 5-Aminoorotic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62930.1M sodium citrate tribasic dihydrate pH 5.6, 1.1M lithium sulfate, 0.45M amonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.264α = 90
b = 141.264β = 90
c = 68.743γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.437LNLSD03B-MX1

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
11.9635.311000.1180.11814.37.6562512.521.052
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)
1.962.071000.6510.6512.97.48154

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3GYE1.9631.415336928521000.160240.158260.19785RANDOM20.561
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.607
r_dihedral_angle_4_deg15.048
r_dihedral_angle_3_deg12.659
r_dihedral_angle_1_deg6.284
r_scangle_it5.685
r_scbond_it3.936
r_mcangle_it2.338
r_mcbond_it1.487
r_angle_refined_deg1.169
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.607
r_dihedral_angle_4_deg15.048
r_dihedral_angle_3_deg12.659
r_dihedral_angle_1_deg6.284
r_scangle_it5.685
r_scbond_it3.936
r_mcangle_it2.338
r_mcbond_it1.487
r_angle_refined_deg1.169
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4645
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms121

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling