5Y9A

Crystal structure of the complex of peptidyl tRNA hydrolase with a phosphate ion at the substrate binding site and cytarabine at a new ligand binding site at 1.1 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0238.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34α = 90
b = 66.16β = 90
c = 76.15γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirror2013-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.116.8596.913.33.868259
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.16

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 REPLACEMENTTHROUGHOUT4LWR1.116.8564713345496.650.127120.125430.1593RANDOM15.136
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]
-0.16-0.090.25
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free48.807
r_dihedral_angle_2_deg34.348
r_sphericity_bonded12.629
r_dihedral_angle_3_deg11.871
r_rigid_bond_restr10.748
r_dihedral_angle_4_deg7.626
r_long_range_B_refined5.996
r_dihedral_angle_1_deg5.923
r_long_range_B_other5.032
r_scangle_other3.96
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free48.807
r_dihedral_angle_2_deg34.348
r_sphericity_bonded12.629
r_dihedral_angle_3_deg11.871
r_rigid_bond_restr10.748
r_dihedral_angle_4_deg7.626
r_long_range_B_refined5.996
r_dihedral_angle_1_deg5.923
r_long_range_B_other5.032
r_scangle_other3.96
r_scbond_other3.394
r_scbond_it3.391
r_angle_other_deg3.272
r_mcangle_other2.999
r_mcangle_it2.995
r_mcbond_other2.589
r_mcbond_it2.587
r_angle_refined_deg2.166
r_chiral_restr0.17
r_bond_refined_d0.029
r_gen_planes_other0.02
r_gen_planes_refined0.013
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 Atoms1496
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing