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Crystal structure of the E.coli LeuRS-tRNA complex with the non- cognate isoleucyl adenylate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AQ7 PDB ENTRY 4AQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M BIS-TRIS (PH 5.5), 23-25 % PEG 3350, 0-200 MM AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.2 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.62 α = 90 b = 67.58 β = 105 c = 224.59 γ = 90
Symmetry Space Group C 1 2 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 2012-05-11 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 2.5 15 97.1 0.17 7 3.2 76242
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 2.5 2.57 98.7 0.68 1.8 3.18
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 ENTRY 4AQ7 2.5 46.49 72414 3828 97.09 0.21759 0.21373 0.2139 0.2902 0.2897 RANDOM 49.695
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] -2.69 0.29 0.66 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.255 r_dihedral_angle_3_deg 20.508 r_dihedral_angle_4_deg 17.544 r_dihedral_angle_1_deg 6.988 r_angle_refined_deg 1.502 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.255 r_dihedral_angle_3_deg 20.508 r_dihedral_angle_4_deg 17.544 r_dihedral_angle_1_deg 6.988 r_angle_refined_deg 1.502 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13669 Nucleic Acid Atoms 3446 Solvent Atoms 306 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing