2Q7G

Pyrrolysine tRNA Synthetase bound to a pyrrolysine analogue (cyc) and ATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5289100 mM Tris 10% PEG2000 MME, pH 7.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.3963.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.773α = 90
b = 104.773β = 90
c = 71.594γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97917NSLSX29A

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
11.94099.60.07829.310.8355923310411
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)
11.91.9796.50.3285.27.5

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.94033104173099.850.163740.162350.18943RANDOM35.272
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]
-0.55-0.27-0.550.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.199
r_dihedral_angle_4_deg13.094
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg6.047
r_scangle_it5.814
r_scbond_it4.453
r_mcangle_it4.354
r_mcbond_it3.946
r_angle_refined_deg1.282
r_mcbond_other0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.199
r_dihedral_angle_4_deg13.094
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg6.047
r_scangle_it5.814
r_scbond_it4.453
r_mcangle_it4.354
r_mcbond_it3.946
r_angle_refined_deg1.282
r_mcbond_other0.92
r_angle_other_deg0.812
r_symmetry_vdw_other0.242
r_nbd_refined0.206
r_nbd_other0.195
r_symmetry_vdw_refined0.18
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.148
r_nbtor_other0.085
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms2046
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing