3G1Z

Structure of IDP01693/yjeA, a potential t-RNA synthetase from Salmonella typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModelSwiss-model (http://swissmodel.expasy.org/SWISS-MODEL.html) model using the input protein sequence

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52951.6 M Sodium/Potassium dihydrogen phosphate, 0.1 M HEPES, pH 7.5, 0.5 mM ATP and 0.3 mM MgCl2, cryoprotected in N-Paratone oil , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2445.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.901α = 90
b = 68.905β = 110.31
c = 73.27γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2008-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

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
11.855096.10.14620.054562645404422.8
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)
11.851.9285.80.5613.824.14784

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 REPLACEMENTTHROUGHOUTSwiss-model (http://swissmodel.expasy.org/SWISS-MODEL.html) model using the input protein sequence1.9547.5143960233997.020.18410.181120.2392RANDOM25.664
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]
-0.05-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.913
r_dihedral_angle_4_deg17.112
r_dihedral_angle_3_deg15.588
r_dihedral_angle_1_deg5.984
r_scangle_it3
r_scbond_it1.995
r_angle_refined_deg1.436
r_mcangle_it1.167
r_mcbond_it0.724
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.913
r_dihedral_angle_4_deg17.112
r_dihedral_angle_3_deg15.588
r_dihedral_angle_1_deg5.984
r_scangle_it3
r_scbond_it1.995
r_angle_refined_deg1.436
r_mcangle_it1.167
r_mcbond_it0.724
r_nbtor_refined0.301
r_nbd_refined0.205
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.147
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms5012
Nucleic Acid Atoms
Solvent Atoms645
Heterogen Atoms77

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling