2Q7E

The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5289100mM Tris 10% PEG2000 MME , pH 7.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.3563.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.124α = 90
b = 105.124β = 90
c = 70.314γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315si 1112007-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97917APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.84098.750.04848.210.6406333848511
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8695.70.87927.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSIRASTHROUGHOUT1.834.438485204298.750.167270.165950.19119RANDOM37.263
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]
-0.52-0.26-0.520.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.606
r_dihedral_angle_4_deg13.33
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg6.218
r_scangle_it6.182
r_mcangle_it4.654
r_scbond_it4.63
r_mcbond_it4.138
r_angle_refined_deg1.297
r_mcbond_other1.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.606
r_dihedral_angle_4_deg13.33
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg6.218
r_scangle_it6.182
r_mcangle_it4.654
r_scbond_it4.63
r_mcbond_it4.138
r_angle_refined_deg1.297
r_mcbond_other1.024
r_angle_other_deg0.842
r_symmetry_vdw_other0.247
r_nbd_refined0.209
r_nbd_other0.191
r_nbtor_refined0.173
r_symmetry_hbond_refined0.147
r_xyhbond_nbd_refined0.146
r_symmetry_vdw_refined0.144
r_nbtor_other0.082
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2105
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing