5LQS

Structure of quinolinate synthase Y21F mutant in complex with substrate-derived quinolinate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298PEG3350, ammonium sulfate, oxaloacetate, DHAP, NaCl, anaerobic
Crystal Properties
Matthews coefficientSolvent content
2.1542.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.06α = 90
b = 48.74β = 103.67
c = 60.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979736ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.943.7398.60.0940.98915.23.623026
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)
11.91.9797.80.5880.5512.93.6

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 REPLACEMENTTHROUGHOUT4P3X1.94021850117598.580.177920.175940.21439RANDOM21.143
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]
0.37-0.3-0.30.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.833
r_dihedral_angle_4_deg20.888
r_dihedral_angle_3_deg13.553
r_long_range_B_refined6.234
r_long_range_B_other5.974
r_dihedral_angle_1_deg5.64
r_scangle_other3.182
r_mcangle_other2.222
r_mcangle_it2.213
r_scbond_it1.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.833
r_dihedral_angle_4_deg20.888
r_dihedral_angle_3_deg13.553
r_long_range_B_refined6.234
r_long_range_B_other5.974
r_dihedral_angle_1_deg5.64
r_scangle_other3.182
r_mcangle_other2.222
r_mcangle_it2.213
r_scbond_it1.931
r_scbond_other1.931
r_angle_refined_deg1.574
r_mcbond_it1.4
r_mcbond_other1.399
r_angle_other_deg1.085
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2401
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing