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Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KJZ PDB ENTRY 3KJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20mM Tris-HCl, 1mM EDTA, 50mM NaCl, 10% isopropanol, 30% PEG 1500, 5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.909 α = 90 b = 58.943 β = 90 c = 61.854 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH MIRROR 2009-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.514
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 2.22 42.67 95.6 0.078 11.9 8170 8170 32.3
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 2.22 2.3 89.4 0.641 2
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 PDB ENTRY 3KJZ 2.22 14.96 8170 7744 379 95.53 0.193 0.19293 0.1916 0.1898 0.21818 0.216 RANDOM 36.27
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] 0.59 -0.41 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.979 r_dihedral_angle_4_deg 17.788 r_dihedral_angle_3_deg 16.984 r_scangle_it 3.164 r_mcangle_it 2.323 r_scbond_it 1.973 r_angle_refined_deg 1.707 r_dihedral_angle_1_deg 1.602 r_mcbond_it 1.296 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.979 r_dihedral_angle_4_deg 17.788 r_dihedral_angle_3_deg 16.984 r_scangle_it 3.164 r_mcangle_it 2.323 r_scbond_it 1.973 r_angle_refined_deg 1.707 r_dihedral_angle_1_deg 1.602 r_mcbond_it 1.296 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1428 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction AMoRE phasing REFMAC refinement SCALEPACK data scaling