3EWY

K314A mutant of human orotidyl-5'-monophosphate decarboxylase soaked with OMP, decarboxylated to UMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP83000.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K
Crystal Properties
Matthews coefficientSolvent content
2.4950.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.12α = 90
b = 116.7β = 90
c = 61.82γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.144.895.10.04810.85.1108733
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1251.60.4691.10.91550

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 REPLACEMENTTHROUGHOUT1.142.4599960532692.140.133820.132870.15184RANDOM14.91
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]
2.34-1.15-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg15.889
r_dihedral_angle_3_deg13.075
r_sphericity_free8.201
r_dihedral_angle_1_deg6.062
r_scangle_it5.371
r_sphericity_bonded4.205
r_scbond_it3.59
r_mcangle_it2.405
r_rigid_bond_restr1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg15.889
r_dihedral_angle_3_deg13.075
r_sphericity_free8.201
r_dihedral_angle_1_deg6.062
r_scangle_it5.371
r_sphericity_bonded4.205
r_scbond_it3.59
r_mcangle_it2.405
r_rigid_bond_restr1.87
r_angle_refined_deg1.79
r_mcbond_it1.686
r_angle_other_deg1.42
r_mcbond_other1.19
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1963
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms33

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling