8I2M

The crystal structure of homodimeric E. coli tryptophanyl-tRNA synthetase bound with niraparib at one of its two active sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2900.16M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.656α = 90
b = 79.761β = 106.32
c = 77.338γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELRIGAKU HyPix-6000HE2022-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.15099.90.1210.0520.99411.1542029
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.211000.570.310.7663.2

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 REPLACEMENTTHROUGHOUT5V0I2.15039904209599.830.203130.20150.23439RANDOM20.242
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]
-0.830.241.36-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.928
r_dihedral_angle_4_deg17.431
r_dihedral_angle_3_deg11.561
r_dihedral_angle_1_deg5.254
r_long_range_B_refined2.324
r_long_range_B_other2.19
r_angle_refined_deg1.135
r_mcangle_it0.995
r_mcangle_other0.994
r_angle_other_deg0.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.928
r_dihedral_angle_4_deg17.431
r_dihedral_angle_3_deg11.561
r_dihedral_angle_1_deg5.254
r_long_range_B_refined2.324
r_long_range_B_other2.19
r_angle_refined_deg1.135
r_mcangle_it0.995
r_mcangle_other0.994
r_angle_other_deg0.875
r_scangle_other0.845
r_mcbond_it0.549
r_mcbond_other0.547
r_scbond_it0.481
r_scbond_other0.478
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5046
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
CrysalisProdata reduction