2O5R

Crystal structure of Glutamyl-tRNA synthetase 1 (EC 6.1.1.17) (Glutamate-tRNA ligase 1) (GluRS 1) (TM1351) from Thermotoga maritima at 2.5 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G59pdb entry 1G59 Chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP82770.2M CaAcetate, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5365.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.953α = 90
b = 69.953β = 90
c = 283.945γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-08-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.94926, 0.97925, 0.97939APS23-ID-D

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
12.3447.35199.90.1656.63528446.8
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)
12.342.421000.0121.67.263322

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 DIFFRACTIONMAD, MOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1G59 Chain A2.3447.35130264152485.960.2360.2340.268RANDOM23.855
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]
-0.18-0.09-0.180.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.887
r_dihedral_angle_4_deg11.053
r_dihedral_angle_3_deg10.179
r_dihedral_angle_1_deg3.06
r_angle_refined_deg1.427
r_angle_other_deg1.235
r_scangle_it0.998
r_scbond_it0.662
r_mcangle_it0.528
r_mcbond_it0.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.887
r_dihedral_angle_4_deg11.053
r_dihedral_angle_3_deg10.179
r_dihedral_angle_1_deg3.06
r_angle_refined_deg1.427
r_angle_other_deg1.235
r_scangle_it0.998
r_scbond_it0.662
r_mcangle_it0.528
r_mcbond_it0.347
r_nbtor_refined0.146
r_nbd_refined0.144
r_nbd_other0.117
r_symmetry_vdw_other0.111
r_symmetry_vdw_refined0.104
r_chiral_restr0.083
r_xyhbond_nbd_refined0.078
r_nbtor_other0.067
r_mcbond_other0.044
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3828
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms9

Software

Software
Software NamePurpose
SHELXphasing
SOLVEphasing
MOLREPphasing
RESOLVEphasing
REFMACrefinement
XSCALEdata scaling
MolProbitymodel building
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing