X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PRYPDB ENTRY 2PRY (S. cerevisiae OPRTase apo form)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4293.1528% PEG 6000, 0.08M magnesium acetate, 0.1M Tris HCl, 2.5mM magnesium chloride, 5.0mM OMP, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4349.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.063α = 90
b = 99.475β = 90
c = 111.995γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-03-31MSINGLE 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
11.895095.20.0530.04811.75.177826740910.227.025
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)
1.891.9666.40.4220.3762.43.95115

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 2PRY (S. cerevisiae OPRTase apo form)1.895507692673711371595.820.230.2290.262RANDOM29.996
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]
0.921.16-2.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.591
r_dihedral_angle_4_deg18.75
r_dihedral_angle_3_deg14.849
r_dihedral_angle_1_deg5.034
r_scangle_it1.745
r_scbond_it1.081
r_angle_refined_deg1.046
r_mcangle_it0.87
r_mcbond_it0.499
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.591
r_dihedral_angle_4_deg18.75
r_dihedral_angle_3_deg14.849
r_dihedral_angle_1_deg5.034
r_scangle_it1.745
r_scbond_it1.081
r_angle_refined_deg1.046
r_mcangle_it0.87
r_mcbond_it0.499
r_nbtor_refined0.299
r_nbd_refined0.187
r_symmetry_hbond_refined0.135
r_symmetry_vdw_refined0.125
r_xyhbond_nbd_refined0.112
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6656
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms100

Software

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