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Crystal structure of Thermus thermophilus peptidyl-tRNA hydrolase in complex with adenosine 5'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.9 M K/Na tartrate, 0.1 M MES buffer pH5.8, and 40 mM adenosine 5'-monophosphate
Crystal Properties Matthews coefficient Solvent content 3.17 61.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.315 α = 90 b = 120.315 β = 90 c = 185.981 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2012-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.6 104.2 99.9 0.056 83.5 21.2 104619
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 1.6 1.63 100 0.214 20.8 20.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.6 104.2 99300 5230 99.87 0.14533 0.14415 0.1588 0.16756 0.1805 RANDOM 19.882
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] 0.15 0.07 0.15 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.433 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 13.766 r_long_range_B_refined 6.99 r_dihedral_angle_1_deg 6.822 r_long_range_B_other 6.804 r_scangle_other 5.516 r_scbond_it 3.819 r_scbond_other 3.818 r_angle_refined_deg 2.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.433 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 13.766 r_long_range_B_refined 6.99 r_dihedral_angle_1_deg 6.822 r_long_range_B_other 6.804 r_scangle_other 5.516 r_scbond_it 3.819 r_scbond_other 3.818 r_angle_refined_deg 2.908 r_mcangle_it 2.892 r_mcangle_other 2.891 r_mcbond_it 2.164 r_mcbond_other 2.152 r_angle_other_deg 1.276 r_chiral_restr 0.169 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d 0.003 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 4320 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing