2PS1

S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and PRPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PRZPDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6288.1538% PEG 4000, 0.14M ammonium acetate, 0.1M sodium acetate, 2.0mM magnesium chloride, 5.0mM PRPP, 5.0mM orotic acid, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K
Crystal Properties
Matthews coefficientSolvent content
2.0439.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.788α = 90.59
b = 50.051β = 105.88
c = 50.078γ = 92.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.98APS19-ID

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
11.755092.90.0490.04317.83.639461366600.221.245
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)
11.751.8163.70.2510.2113.22.52533

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP)1.7549.943953436660184492.730.1950.1950.1940.217RANDOM23.628
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]
0.240.091.140.320.630.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.196
r_dihedral_angle_3_deg14.733
r_dihedral_angle_4_deg10.863
r_dihedral_angle_1_deg4.831
r_scangle_it1.536
r_angle_refined_deg1.11
r_scbond_it0.982
r_mcangle_it0.853
r_mcbond_it0.484
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.196
r_dihedral_angle_3_deg14.733
r_dihedral_angle_4_deg10.863
r_dihedral_angle_1_deg4.831
r_scangle_it1.536
r_angle_refined_deg1.11
r_scbond_it0.982
r_mcangle_it0.853
r_mcbond_it0.484
r_nbtor_refined0.298
r_nbd_refined0.18
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.091
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3446
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms68

Software

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