5AYZ

CRYSTAL STRUCTURE OF HUMAN QUINOLINATE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH THE PRODUCT NICOTINATE MONONUCLEOTIDE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LAR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529410% PEG MME 2K, 0.01M POTASSIUM THIOCYANATE, PH 5.0, VAPOR DIFFUSION, TEMPERATURE 273.0K
Crystal Properties
Matthews coefficientSolvent content
2.1843.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.186α = 90
b = 101.156β = 92.49
c = 151.643γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9795PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.65099.28.46.6957271
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6794.1

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 REPLACEMENTTHROUGHOUT3LAR2.644.1495727503699.20.2270.2260.256RANDOM31.09
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]
-0.06-0.050.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.423
r_dihedral_angle_4_deg20.261
r_dihedral_angle_3_deg19.097
r_dihedral_angle_1_deg7.394
r_angle_refined_deg2.05
r_angle_other_deg1.792
r_chiral_restr0.133
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.423
r_dihedral_angle_4_deg20.261
r_dihedral_angle_3_deg19.097
r_dihedral_angle_1_deg7.394
r_angle_refined_deg2.05
r_angle_other_deg1.792
r_chiral_restr0.133
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.01
r_gen_planes_other0.01
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25296
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing