3EWX

K314A mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, degraded to BMP


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
2.4850.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.75α = 90
b = 116.72β = 90
c = 61.8γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-04MSINGLE 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
11.434.7999.70.097116.655483
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)
11.41.4294.60.6561.33.11083

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 REPLACEMENTTHROUGHOUT1.434.7952007277898.480.151670.150290.17789RANDOM11.235
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]
1.98-1.01-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.819
r_dihedral_angle_4_deg15.134
r_dihedral_angle_3_deg13.124
r_dihedral_angle_1_deg5.893
r_sphericity_free4.957
r_scangle_it4.177
r_scbond_it2.643
r_sphericity_bonded1.951
r_mcangle_it1.607
r_angle_refined_deg1.368
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.819
r_dihedral_angle_4_deg15.134
r_dihedral_angle_3_deg13.124
r_dihedral_angle_1_deg5.893
r_sphericity_free4.957
r_scangle_it4.177
r_scbond_it2.643
r_sphericity_bonded1.951
r_mcangle_it1.607
r_angle_refined_deg1.368
r_rigid_bond_restr1.269
r_mcbond_it0.996
r_angle_other_deg0.913
r_mcbond_other0.386
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1966
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms28

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling