2AG6

Crystal structure of p-bromo-l-phenylalanine-tRNA sythetase in complex with p-bromo-l-phenylalanine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZH6PDB Entry 1ZH6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320% PEG-300, %% PEG-8000, 10% GLYCEROL, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.719α = 90
b = 102.719β = 90
c = 70.598γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.0ALS5.0.3

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
11.9800.07239.95
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)
11.91.9798.30.7414.754.3

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB Entry 1ZH61.972.5528644153899.520.211370.209470.24736RANDOM37.762
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]
0.920.92-1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.746
r_dihedral_angle_3_deg17.541
r_dihedral_angle_4_deg16.226
r_dihedral_angle_1_deg5.85
r_scangle_it5.59
r_scbond_it4.165
r_mcangle_it1.758
r_mcbond_it1.567
r_angle_refined_deg1.511
r_angle_other_deg0.837
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.746
r_dihedral_angle_3_deg17.541
r_dihedral_angle_4_deg16.226
r_dihedral_angle_1_deg5.85
r_scangle_it5.59
r_scbond_it4.165
r_mcangle_it1.758
r_mcbond_it1.567
r_angle_refined_deg1.511
r_angle_other_deg0.837
r_mcbond_other0.321
r_symmetry_vdw_refined0.254
r_symmetry_hbond_refined0.25
r_nbd_refined0.224
r_symmetry_vdw_other0.206
r_nbtor_refined0.188
r_nbd_other0.185
r_xyhbond_nbd_refined0.162
r_chiral_restr0.1
r_nbtor_other0.091
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms2462
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling