2Q5H

Crystal structure of apo-wildtype Glycyl-tRNA synthetase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG 3350, 0.2M Sodium bromide, 0.1M Bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3763.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.53α = 90
b = 92.53β = 90
c = 246.86γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2005-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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
133095.60.18610.39.221172
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)
133.11900.9861.881941

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 1ATI329.2720082102194.60.207490.205260.25013RANDOM31.316
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]
0.30.3-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.579
r_dihedral_angle_4_deg16.713
r_dihedral_angle_3_deg16.347
r_scangle_it7.564
r_dihedral_angle_1_deg5.722
r_scbond_it5.095
r_mcangle_it3.966
r_mcbond_it2.877
r_angle_refined_deg1.004
r_angle_other_deg0.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.579
r_dihedral_angle_4_deg16.713
r_dihedral_angle_3_deg16.347
r_scangle_it7.564
r_dihedral_angle_1_deg5.722
r_scbond_it5.095
r_mcangle_it3.966
r_mcbond_it2.877
r_angle_refined_deg1.004
r_angle_other_deg0.773
r_mcbond_other0.555
r_symmetry_vdw_refined0.223
r_nbd_refined0.216
r_symmetry_vdw_other0.185
r_nbd_other0.181
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.099
r_symmetry_hbond_refined0.084
r_nbtor_other0.082
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms4213
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms

Software

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