2EAW

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DQW 

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
2.0138.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.571α = 90
b = 59.37β = 114.3
c = 69.863γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.54

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
12.8863.6797.80.14140.1714.291.841159811348
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)
2.882.928.90.40.54542.040.49232

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DQW2.8863.63110291039852294.280.261790.261790.259460.30737RANDOM10.041
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]
2.072.38-1.841.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg19.021
r_dihedral_angle_4_deg18.059
r_dihedral_angle_1_deg8.528
r_scangle_it3.588
r_scbond_it2.12
r_angle_refined_deg1.993
r_mcangle_it1.326
r_mcbond_it0.892
r_symmetry_hbond_refined0.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg19.021
r_dihedral_angle_4_deg18.059
r_dihedral_angle_1_deg8.528
r_scangle_it3.588
r_scbond_it2.12
r_angle_refined_deg1.993
r_mcangle_it1.326
r_mcbond_it0.892
r_symmetry_hbond_refined0.356
r_nbtor_refined0.343
r_symmetry_vdw_refined0.337
r_chiral_restr0.32
r_nbd_refined0.274
r_xyhbond_nbd_refined0.171
r_bond_refined_d0.025
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3916
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
PHASERphasing