5AH5 | pdb_00005ah5

Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BTEPDB ENTRIES 2BTE, 4AS1
experimental modelPDB 4AS1PDB ENTRIES 2BTE, 4AS1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 27 % PEG 5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.958.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.91α = 90
b = 50.32β = 93.48
c = 170.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.148.699.40.0810.63.71603302
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)
12.12.1599.60.762.13.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 2BTE, 4AS12.148.58160330848799.460.196340.194160.20.237320.24RANDOM50.507
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]
0.16-0.79-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.35
r_dihedral_angle_4_deg17.687
r_dihedral_angle_3_deg15.711
r_long_range_B_refined9.179
r_long_range_B_other9.164
r_dihedral_angle_1_deg7.705
r_scangle_other7.005
r_mcangle_it5.798
r_mcangle_other5.798
r_scbond_it4.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.35
r_dihedral_angle_4_deg17.687
r_dihedral_angle_3_deg15.711
r_long_range_B_refined9.179
r_long_range_B_other9.164
r_dihedral_angle_1_deg7.705
r_scangle_other7.005
r_mcangle_it5.798
r_mcangle_other5.798
r_scbond_it4.663
r_scbond_other4.644
r_mcbond_it4.058
r_mcbond_other4.058
r_angle_refined_deg1.736
r_angle_other_deg1.137
r_chiral_restr0.112
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12364
Nucleic Acid Atoms3423
Solvent Atoms871
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing