3C2V

Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG 3350, 0.2 M ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4650.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.668α = 90
b = 154.668β = 90
c = 69.346γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDBRUKER SMART 20002005-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5418

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
12.35099.20.0830.0833.954.614205140891150.6
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)
2.32.3898.40.390.393.9541388

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2944.631281851490.990.2270.2250.282RANDOM50.579
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]
-5.24-2.62-5.247.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.358
r_dihedral_angle_4_deg19.919
r_dihedral_angle_3_deg15.1
r_dihedral_angle_1_deg12.026
r_scangle_it3.093
r_scbond_it2.131
r_mcangle_it1.704
r_angle_refined_deg1.675
r_mcbond_it0.983
r_chiral_restr0.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.358
r_dihedral_angle_4_deg19.919
r_dihedral_angle_3_deg15.1
r_dihedral_angle_1_deg12.026
r_scangle_it3.093
r_scbond_it2.131
r_mcangle_it1.704
r_angle_refined_deg1.675
r_mcbond_it0.983
r_chiral_restr0.578
r_nbtor_refined0.336
r_nbd_refined0.313
r_symmetry_hbond_refined0.282
r_symmetry_vdw_refined0.268
r_xyhbond_nbd_refined0.196
r_bond_refined_d0.009
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2067
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction