☰ Navigation Tabs
Structure of pyrrolysyl-tRNA synthetase in complex with adenylated butyryl lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BWA PDB ENTRY 4BWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 0.1 M LIAC, 12% PEG3350, pH 7.4
Crystal Properties Matthews coefficient Solvent content 3.8 67.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.257 α = 90 b = 105.257 β = 90 c = 71.382 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2013-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.28 38.44 99.9 0.04 24.69 6 20634 1.5
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 2.28 2.36 100 0.45 3.86 6.3
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 4BWA 2.28 38.44 19600 1034 99.91 0.17733 0.17627 0.1797 0.19666 0.1933 RANDOM 49.551
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] -0.48 -0.48 -0.48 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 13.357 r_dihedral_angle_1_deg 6.149 r_mcangle_it 3.248 r_scbond_it 2.389 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.378 r_angle_other_deg 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 13.357 r_dihedral_angle_1_deg 6.149 r_mcangle_it 3.248 r_scbond_it 2.389 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.378 r_angle_other_deg 0.751 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other 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 2096 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling