5LQM

Structure of quinolinate synthase Y21F mutant in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298PEG3350, sodium citrate, KCl, anaerobic
Crystal Properties
Matthews coefficientSolvent content
2.1843.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.807α = 90
b = 48.936β = 104.62
c = 60.422γ = 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)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
11.6237.53910.0440.998122.534681
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)
11.621.68620.4540.491.82.4

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 REPLACEMENTTHROUGHOUT4P3X1.6237.5332948173390.950.152120.149450.20136RANDOM23.029
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]
1.33-1.16-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg5.27
r_mcangle_other2.488
r_mcangle_it2.478
r_scangle_other2.476
r_scbond_it2.136
r_scbond_other2.129
r_angle_refined_deg1.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg5.27
r_mcangle_other2.488
r_mcangle_it2.478
r_scangle_other2.476
r_scbond_it2.136
r_scbond_other2.129
r_angle_refined_deg1.535
r_angle_other_deg1
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2401
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing