4S03

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.752930.1 M sodium citrate, 15% PEG 6000, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.506α = 90
b = 79.098β = 90
c = 91.273γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
12.055099.60.1169.65.312224
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)
12.052.1178.70.5312.35.1930

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 REPLACEMENTTHROUGHOUTPDB entry 1y2q2.0531.581163858699.390.167570.166050.19939RANDOM27.504
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]
-4.9-6.9211.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg17.011
r_dihedral_angle_3_deg14.555
r_long_range_B_refined7.525
r_long_range_B_other7.32
r_dihedral_angle_1_deg6.957
r_scangle_other4.957
r_scbond_it3.149
r_scbond_other3.147
r_mcangle_it2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg17.011
r_dihedral_angle_3_deg14.555
r_long_range_B_refined7.525
r_long_range_B_other7.32
r_dihedral_angle_1_deg6.957
r_scangle_other4.957
r_scbond_it3.149
r_scbond_other3.147
r_mcangle_it2.67
r_mcangle_other2.668
r_mcbond_other1.835
r_mcbond_it1.833
r_angle_refined_deg1.62
r_angle_other_deg0.812
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms1119
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata scaling