9EG9 | pdb_00009eg9

Crystal structure of human dihydroorotate dehydrogenase in complex with lapachol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K9C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.8293.150.1 M sodium acetate trihydrate pH 4.8, 1.8 M ammonium sulfate and 30% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
3.6366.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.46α = 90
b = 90.46β = 90
c = 122.66γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2024-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918400BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.3148.34100118.4519.9613928322.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.311.391000.4120.98

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3148.34132428685599.940.174270.173980.18350.179970.1899RANDOM20.329
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]
0.280.140.28-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.976
r_dihedral_angle_4_deg18.204
r_dihedral_angle_3_deg11.876
r_dihedral_angle_1_deg6.123
r_long_range_B_refined4.727
r_long_range_B_other4.497
r_scangle_other2.784
r_mcangle_it1.89
r_mcangle_other1.89
r_scbond_it1.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.976
r_dihedral_angle_4_deg18.204
r_dihedral_angle_3_deg11.876
r_dihedral_angle_1_deg6.123
r_long_range_B_refined4.727
r_long_range_B_other4.497
r_scangle_other2.784
r_mcangle_it1.89
r_mcangle_other1.89
r_scbond_it1.842
r_scbond_other1.841
r_angle_refined_deg1.456
r_angle_other_deg1.426
r_mcbond_it1.184
r_mcbond_other1.183
r_chiral_restr0.071
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2727
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
pointlessdata scaling
XDSdata reduction
PHASERphasing