3C2R

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29820% PEG 3350, 0.2 M potassium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.524α = 90
b = 155.524β = 90
c = 121.072γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 325 mm CCD2005-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.446.9321000.0990.0996.410.922088220881150
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)
2.42.461000.5780.5781.3111622

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 REPLACEMENTTHROUGHOUT2.446.9321560218997.620.1880.1830.225RANDOM50.701
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]
-1.28-0.64-1.281.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.526
r_scangle_it25.389
r_scbond_it24.872
r_dihedral_angle_4_deg21.9
r_dihedral_angle_3_deg18.412
r_mcangle_it17.27
r_mcbond_it15.399
r_dihedral_angle_1_deg2.079
r_angle_refined_deg1.937
r_nbtor_refined0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.526
r_scangle_it25.389
r_scbond_it24.872
r_dihedral_angle_4_deg21.9
r_dihedral_angle_3_deg18.412
r_mcangle_it17.27
r_mcbond_it15.399
r_dihedral_angle_1_deg2.079
r_angle_refined_deg1.937
r_nbtor_refined0.34
r_nbd_refined0.306
r_symmetry_vdw_refined0.279
r_xyhbond_nbd_refined0.205
r_symmetry_hbond_refined0.181
r_chiral_restr0.123
r_bond_refined_d0.018
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4082
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms24

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction