2V30

Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (UMPS) in complex with its product UMP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JGYPDB ENTRY 2JGY

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.6553.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.103α = 90
b = 77.853β = 90
c = 153.209γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
122099.90.0735.614.149400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.111000.2112.614.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JGY219.644685124821000.1550.1530.188RANDOM17.42
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]
-0.491.59-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_3_deg13.311
r_dihedral_angle_4_deg12.577
r_dihedral_angle_1_deg6.016
r_scangle_it3.568
r_scbond_it2.637
r_mcangle_it1.59
r_mcbond_it1.444
r_angle_refined_deg1.338
r_angle_other_deg0.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.914
r_dihedral_angle_3_deg13.311
r_dihedral_angle_4_deg12.577
r_dihedral_angle_1_deg6.016
r_scangle_it3.568
r_scbond_it2.637
r_mcangle_it1.59
r_mcbond_it1.444
r_angle_refined_deg1.338
r_angle_other_deg0.949
r_symmetry_vdw_other0.316
r_symmetry_vdw_refined0.209
r_nbd_refined0.2
r_nbd_other0.193
r_xyhbond_nbd_refined0.176
r_symmetry_hbond_refined0.17
r_nbtor_refined0.166
r_nbtor_other0.083
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3974
Nucleic Acid Atoms
Solvent Atoms574
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing