3PD4

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with glycyl-3'-aminoadenosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG 3350, Bis-Tris, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9737.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.335α = 90
b = 69.083β = 90
c = 94.659γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2009-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.42598.70.10915.24.6108121081222
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)
2.42.4987.60.2913.53.9

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 1Y2Q2.424.851025452199.490.20760.203680.28924RANDOM32.397
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]
0.962.65-3.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_3_deg17.713
r_dihedral_angle_4_deg17.289
r_dihedral_angle_1_deg6.675
r_scangle_it3.465
r_scbond_it2.074
r_angle_refined_deg1.594
r_mcangle_it1.207
r_mcbond_it0.714
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_3_deg17.713
r_dihedral_angle_4_deg17.289
r_dihedral_angle_1_deg6.675
r_scangle_it3.465
r_scbond_it2.074
r_angle_refined_deg1.594
r_mcangle_it1.207
r_mcbond_it0.714
r_nbtor_refined0.303
r_symmetry_vdw_refined0.237
r_nbd_refined0.215
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.157
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2279
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms46

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement