5F33

Structure of quinolinate synthase in complex with phosphoglycolohydroxamate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.8298PEG3350, Tris, LiSO4, KCl, PGH anaerobic
Crystal Properties
Matthews coefficientSolvent content
2.1643.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.094α = 90
b = 49.16β = 104.1
c = 60.221γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.96862ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.4549.1698.60.040.0340.998122.851724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.598.70.5550.5561.72.8

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 REPLACEMENTTHROUGHOUT4P3X1.453049128257498.460.143690.141410.18627RANDOM22.337
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]
0.47-0.65-0.220.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.254
r_sphericity_free24.485
r_dihedral_angle_4_deg14.559
r_dihedral_angle_3_deg12.91
r_sphericity_bonded8.789
r_rigid_bond_restr8.771
r_dihedral_angle_1_deg5.303
r_angle_other_deg3.49
r_long_range_B_refined3.43
r_long_range_B_other3.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.254
r_sphericity_free24.485
r_dihedral_angle_4_deg14.559
r_dihedral_angle_3_deg12.91
r_sphericity_bonded8.789
r_rigid_bond_restr8.771
r_dihedral_angle_1_deg5.303
r_angle_other_deg3.49
r_long_range_B_refined3.43
r_long_range_B_other3.112
r_scangle_other2.506
r_mcangle_other2.318
r_mcangle_it2.317
r_scbond_it2.133
r_scbond_other2.09
r_mcbond_it1.784
r_mcbond_other1.772
r_angle_refined_deg1.51
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d
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 Atoms2400
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing