3EX4

human orotidyl-5'-monophosphate decarboxylase in complex with 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
2.4850.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.32α = 90
b = 116.9β = 90
c = 62.06γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-05-24MSINGLE 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
11.2444.798.90.07511.86.178072
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)
1.241.2647.10.3591.64.8517

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 REPLACEMENTTHROUGHOUT1.2438.6673733392898.490.119370.118540.13507RANDOM9.62
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]
0.17-0.16-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.723
r_dihedral_angle_4_deg14.111
r_dihedral_angle_3_deg12.932
r_sphericity_free7.292
r_dihedral_angle_1_deg5.947
r_scangle_it4.939
r_scbond_it3.23
r_angle_other_deg3.184
r_sphericity_bonded3.017
r_mcangle_it2.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.723
r_dihedral_angle_4_deg14.111
r_dihedral_angle_3_deg12.932
r_sphericity_free7.292
r_dihedral_angle_1_deg5.947
r_scangle_it4.939
r_scbond_it3.23
r_angle_other_deg3.184
r_sphericity_bonded3.017
r_mcangle_it2.187
r_angle_refined_deg1.607
r_rigid_bond_restr1.523
r_mcbond_it1.438
r_mcbond_other0.714
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms2096
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms22

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling