2P1F

Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EAW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.42932.28M Ammonium sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.314α = 90
b = 116.875β = 90
c = 61.946γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7665.0999.640.0970.09797.82842726969
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.791000.4590.4594.497.81392

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2EAW1.7665.092842726969143599.640.141130.139490.17067RANDOM12.841
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]
0.82-0.41-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.124
r_dihedral_angle_4_deg18.698
r_dihedral_angle_3_deg13.139
r_dihedral_angle_1_deg5.778
r_scangle_it4.329
r_scbond_it2.659
r_angle_refined_deg1.503
r_mcangle_it1.454
r_mcbond_it0.967
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.124
r_dihedral_angle_4_deg18.698
r_dihedral_angle_3_deg13.139
r_dihedral_angle_1_deg5.778
r_scangle_it4.329
r_scbond_it2.659
r_angle_refined_deg1.503
r_mcangle_it1.454
r_mcbond_it0.967
r_nbtor_refined0.309
r_nbd_refined0.23
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.136
r_chiral_restr0.104
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1980
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing