☰ Navigation Tabs
Crystal structure of Thermus thermophilus peptidyl-tRNA hydrolase C-terminal 16 amino acid deletion mutant
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 0.5 M (NH4)2SO4, 0.1 M Tris-HCl pH7.5, 30% (v/v) PEG600, and 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.948 α = 90 b = 81.948 β = 90 c = 123.94 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 PIXEL DECTRIS PILATUS3 S 6M 2015-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980 Photon Factory BL-17A
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 70.97 100 0.062 40.2 18.8 15036
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 2.14 100 0.277 7.5 18
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 2.1 70.97 14220 768 99.95 0.20361 0.20127 0.2133 0.24792 0.2558 RANDOM 39.971
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] 0.28 0.14 0.28 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.654 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 16.654 r_long_range_B_refined 10.27 r_long_range_B_other 10.053 r_scangle_other 7.458 r_dihedral_angle_1_deg 7.374 r_scbond_it 5.284 r_scbond_other 5.142 r_mcangle_it 5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.654 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 16.654 r_long_range_B_refined 10.27 r_long_range_B_other 10.053 r_scangle_other 7.458 r_dihedral_angle_1_deg 7.374 r_scbond_it 5.284 r_scbond_other 5.142 r_mcangle_it 5 r_mcangle_other 4.997 r_mcbond_it 3.977 r_mcbond_other 3.977 r_angle_refined_deg 2.009 r_angle_other_deg 1.102 r_chiral_restr 0.127 r_bond_refined_d 0.019 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 1320 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing