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The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 289 100mM Tris
10% PEG2000 MME
, pH 7.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.35 63.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.124 α = 90 b = 105.124 β = 90 c = 70.314 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 CCD ADSC QUANTUM 315 si 111 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97917 APS 24-ID-C
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 1.8 40 98.75 0.048 48.2 10.6 40633 38485 1 1
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 1.8 1.86 95.7 0.879 2 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 1.8 34.4 38485 2042 98.75 0.16727 0.16595 0.1722 0.19119 0.1983 RANDOM 37.263
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] -0.52 -0.26 -0.52 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.606 r_dihedral_angle_4_deg 13.33 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 6.218 r_scangle_it 6.182 r_mcangle_it 4.654 r_scbond_it 4.63 r_mcbond_it 4.138 r_angle_refined_deg 1.297 r_mcbond_other 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.606 r_dihedral_angle_4_deg 13.33 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 6.218 r_scangle_it 6.182 r_mcangle_it 4.654 r_scbond_it 4.63 r_mcbond_it 4.138 r_angle_refined_deg 1.297 r_mcbond_other 1.024 r_angle_other_deg 0.842 r_symmetry_vdw_other 0.247 r_nbd_refined 0.209 r_nbd_other 0.191 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.144 r_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SOLVE phasing