3EX3

human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, covalent adduct


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
2.4549.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.5α = 90
b = 61.63β = 113.05
c = 70.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-05-15MSINGLE 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
11.4542.3799.20.0778.83.796142
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)
11.451.4897.40.5751.63.33780

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 REPLACEMENTTHROUGHOUT1.4542.3790682478698.550.203390.201690.23565RANDOM14.304
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]
0.331.62-0.91.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.059
r_dihedral_angle_4_deg14.703
r_dihedral_angle_3_deg14.287
r_dihedral_angle_1_deg6.266
r_scangle_it3.808
r_scbond_it2.454
r_angle_refined_deg1.572
r_mcangle_it1.549
r_angle_other_deg0.929
r_mcbond_it0.918
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.059
r_dihedral_angle_4_deg14.703
r_dihedral_angle_3_deg14.287
r_dihedral_angle_1_deg6.266
r_scangle_it3.808
r_scbond_it2.454
r_angle_refined_deg1.572
r_mcangle_it1.549
r_angle_other_deg0.929
r_mcbond_it0.918
r_mcbond_other0.273
r_chiral_restr0.09
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms442
Heterogen Atoms48

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling