2Q5I

Crystal structure of apo S581L Glycyl-tRNA synthetase mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% PEG 3350, 0.2M Na2SO4, 0.1M Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3663.44

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-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2005-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97650ESRFBM14

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
12.83099.80.10820.714.227432
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)
12.82.998.50.7341.55.92643

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 1ATI2.829.2725923132999.860.21440.212650.24919RANDOM34.963
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]
0.450.45-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.791
r_dihedral_angle_4_deg15.649
r_dihedral_angle_3_deg13.743
r_scangle_it7.923
r_scbond_it5.459
r_dihedral_angle_1_deg5.159
r_mcangle_it3.829
r_mcbond_it2.996
r_angle_refined_deg0.987
r_angle_other_deg0.882
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.791
r_dihedral_angle_4_deg15.649
r_dihedral_angle_3_deg13.743
r_scangle_it7.923
r_scbond_it5.459
r_dihedral_angle_1_deg5.159
r_mcangle_it3.829
r_mcbond_it2.996
r_angle_refined_deg0.987
r_angle_other_deg0.882
r_mcbond_other0.581
r_symmetry_hbond_refined0.26
r_nbd_refined0.199
r_nbtor_refined0.177
r_nbd_other0.176
r_symmetry_vdw_refined0.174
r_symmetry_vdw_other0.174
r_chiral_restr0.1
r_xyhbond_nbd_refined0.092
r_nbtor_other0.08
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms4215
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms15

Software

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