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Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Angstrom resolution shows the Closed Structure of the Substrate Binding Cleft
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.024 α = 90.33 b = 43.028 β = 105.78 c = 65.1 γ = 112.51
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH Mirror 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.19 35.37 98.3 0.062 22.2 17325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.23 97.3 0.157 7.6
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 4JC4 2.19 35.37 16439 884 97.88 0.17002 0.16844 0.1715 0.19847 0.1981 RANDOM 17.196
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] 1.14 0.15 0.51 -0.41 0.06 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 17.583 r_angle_other_deg 3.602 r_dihedral_angle_1_deg 3.221 r_mcangle_it 1.687 r_mcangle_other 1.687 r_angle_refined_deg 1.589 r_mcbond_it 1.066 r_mcbond_other 1.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 17.583 r_angle_other_deg 3.602 r_dihedral_angle_1_deg 3.221 r_mcangle_it 1.687 r_mcangle_other 1.687 r_angle_refined_deg 1.589 r_mcbond_it 1.066 r_mcbond_other 1.064 r_chiral_restr 0.137 r_bond_refined_d 0.014 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_scbond_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling