9DHI

DHODH in complex with Compound 7


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.10 M NaAc pH4.8, 2.0 M (NH4)2SO4, 30 % (v/v) Glycerol
Crystal Properties
Matthews coefficientSolvent content
3.5565.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.758α = 90
b = 90.758β = 90
c = 122.778γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2021-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3878.61000.0760.0220.999316.52312.47120423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.4031000.5610.55931.30112.67

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3878.6114648577299.990.117760.116690.13865RANDOM23.981
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]
0.10.050.1-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.792
r_dihedral_angle_4_deg20.521
r_dihedral_angle_3_deg12.104
r_dihedral_angle_1_deg6.274
r_angle_other_deg1.467
r_angle_refined_deg1.444
r_chiral_restr0.084
r_bond_other_d0.009
r_gen_planes_refined0.008
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.792
r_dihedral_angle_4_deg20.521
r_dihedral_angle_3_deg12.104
r_dihedral_angle_1_deg6.274
r_angle_other_deg1.467
r_angle_refined_deg1.444
r_chiral_restr0.084
r_bond_other_d0.009
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2797
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms163

Software

Software
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement