2PRY

Apo form of S. cerevisiae orotate phosphoribosyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1STOPDB ENTRY 1STO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4293.1526% PEG 6000, 0.2M magnesium acetate, 0.1M Tris HCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4549.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.791α = 90
b = 59.791β = 90
c = 135.595γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93.15IMAGE PLATERIGAKU RAXIS IVOsmic confocal2004-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R1.54

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
12.352598.50.0530.05324.410881107180.248.52
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)
12.352.4384.50.2460.2463.7870

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1STO2.3524.92108311066652298.470.2390.2380.26RANDOM49.601
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]
1.021.02-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.101
r_scangle_it2.716
r_mcangle_it1.594
r_scbond_it1.515
r_angle_refined_deg1.065
r_mcbond_it0.865
r_symmetry_vdw_refined0.211
r_nbd_refined0.197
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.101
r_scangle_it2.716
r_mcangle_it1.594
r_scbond_it1.515
r_angle_refined_deg1.065
r_mcbond_it0.865
r_symmetry_vdw_refined0.211
r_nbd_refined0.197
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.162
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1663
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing