☰ Navigation Tabs
Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BTE PDB ENTRIES 2BTE, 4AS1 experimental model PDB 4AS1 PDB ENTRIES 2BTE, 4AS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 27 % PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.9 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.91 α = 90 b = 50.32 β = 93.48 c = 170.52 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2011-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 48.6 99.4 0.08 10.6 3.7 160330 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.6 0.76 2.1 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2BTE, 4AS1 2.1 48.58 160330 8487 99.46 0.19634 0.19416 0.1996 0.23732 0.2406 RANDOM 50.507
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.35 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_3_deg 15.711 r_long_range_B_refined 9.179 r_long_range_B_other 9.164 r_dihedral_angle_1_deg 7.705 r_scangle_other 7.005 r_mcangle_it 5.798 r_mcangle_other 5.798 r_scbond_it 4.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.35 r_dihedral_angle_4_deg 17.687 r_dihedral_angle_3_deg 15.711 r_long_range_B_refined 9.179 r_long_range_B_other 9.164 r_dihedral_angle_1_deg 7.705 r_scangle_other 7.005 r_mcangle_it 5.798 r_mcangle_other 5.798 r_scbond_it 4.663 r_scbond_other 4.644 r_mcbond_it 4.058 r_mcbond_other 4.058 r_angle_refined_deg 1.736 r_angle_other_deg 1.137 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 12364 Nucleic Acid Atoms 3423 Solvent Atoms 871 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing