☰ Navigation Tabs
Crystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PTH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 293 100mM acetate buffer, 20% (w/v) 1,4-butanediol, 30mM glycyl-glycyl-glycine , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.07 α = 90 b = 55.07 β = 90 c = 413.1 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 MARMOSAIC 225 mm CCD 2008-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 98.1 0.056 0.059 24.94 10.9 27129 27129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.54 93.7 0.187 0.2 8.2 8.1 4136
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2PTH 2.4 50 26216 26216 1390 99.82 0.19472 0.19472 0.19251 0.1909 0.23657 0.2289 RANDOM 47.222
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] 3.14 1.57 3.14 -4.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 16.8 r_dihedral_angle_1_deg 5.403 r_scangle_it 2.025 r_angle_refined_deg 1.366 r_scbond_it 1.3 r_mcangle_it 0.936 r_mcbond_it 0.488 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.94 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 16.8 r_dihedral_angle_1_deg 5.403 r_scangle_it 2.025 r_angle_refined_deg 1.366 r_scbond_it 1.3 r_mcangle_it 0.936 r_mcbond_it 0.488 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2960 Nucleic Acid Atoms 1532 Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction