3EX1

human orotidyl-5'-monophosphate decarboxylase soaked with 6-cyano-UMP, converted 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
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.35α = 90
b = 61.85β = 113.69
c = 70.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-08-29MSINGLE 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
11.442.599.80.0747.93.6107488
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)
11.41.4498.50.6021.43.26504

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 REPLACEMENTTHROUGHOUT1.438.27102082538499.780.179350.178660.19258RANDOM14.918
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]
-7.827.83-6.9114.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.581
r_dihedral_angle_4_deg12.738
r_dihedral_angle_3_deg12.566
r_dihedral_angle_1_deg5.807
r_scangle_it3.654
r_scbond_it2.325
r_mcangle_it1.425
r_angle_refined_deg1.405
r_angle_other_deg0.928
r_mcbond_it0.801
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.581
r_dihedral_angle_4_deg12.738
r_dihedral_angle_3_deg12.566
r_dihedral_angle_1_deg5.807
r_scangle_it3.654
r_scbond_it2.325
r_mcangle_it1.425
r_angle_refined_deg1.405
r_angle_other_deg0.928
r_mcbond_it0.801
r_mcbond_other0.208
r_chiral_restr0.087
r_bond_refined_d0.012
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3929
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms50

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling