5F35

Structure of quinolinate synthase in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P3X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4298PEG4000, Na3citrate, NH4acetate, NaCl, anaerobic
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.948α = 90
b = 49.3β = 104.25
c = 62.701γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5749.399.10.19.55.540043
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.6299.10.8411.55.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4P3X1.627.7736433189699.790.130380.127930.17701RANDOM20.114
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]
0.64-0.6-0.25-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.646
r_sphericity_free31.092
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg13.505
r_sphericity_bonded10.26
r_dihedral_angle_1_deg5.176
r_long_range_B_refined4.406
r_long_range_B_other4.014
r_scangle_other3.206
r_scbond_other2.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.646
r_sphericity_free31.092
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg13.505
r_sphericity_bonded10.26
r_dihedral_angle_1_deg5.176
r_long_range_B_refined4.406
r_long_range_B_other4.014
r_scangle_other3.206
r_scbond_other2.611
r_scbond_it2.61
r_mcangle_other2.411
r_mcangle_it2.41
r_mcbond_other1.802
r_mcbond_it1.801
r_rigid_bond_restr1.629
r_angle_refined_deg1.557
r_angle_other_deg1.011
r_chiral_restr0.105
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2402
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing