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Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PTH PDB ENTRY 2PTH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 15%(w/v) PEG 8000, 100mm HEPES, 5%(v/v) 2-propanol, pH 7.5, Microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.81 32.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.84 α = 90 b = 57.06 β = 90 c = 72.59 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 100 IMAGE PLATE MAR scanner 345 mm plate 2006-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.49 30 98.2 0.082 15.14 4.1 5428 37.8
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 2.49 2.58 95 0.384 3.6 522
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 PDB ENTRY 2PTH 2.5 19.01 5397 299 98.3 0.198 0.198 0.1981 0.241 0.2366 RANDOM 35.6
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] -11.35 17.66 -6.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.94 c_mcangle_it 2.19 c_scbond_it 1.98 c_angle_deg 1.4 c_mcbond_it 1.33 c_improper_angle_d 0.85 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1341 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing