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Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z2I PDB ENTRY 2Z2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil 7.5 291 0.1M HEPES, 25% PEG 8000, 5% dioxane, pH 7.5, Microbatch under oil, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.25 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.31 α = 90 b = 60.31 β = 90 c = 87.67 γ = 120
Symmetry Space Group P 32 2 1
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 2010-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.5 30 99.7 0.081 3.9 6725 72.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64
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 2Z2I 2.5 30 6392 320 99.66 0.23747 0.23655 0.2346 0.25541 0.2464 RANDOM 62.471
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] -1.45 -0.72 -1.45 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.119 r_dihedral_angle_3_deg 19.925 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_1_deg 3.983 r_scangle_it 2.38 r_mcangle_it 1.681 r_scbond_it 1.553 r_angle_refined_deg 1.546 r_mcbond_it 0.982 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.119 r_dihedral_angle_3_deg 19.925 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_1_deg 3.983 r_scangle_it 2.38 r_mcangle_it 1.681 r_scbond_it 1.553 r_angle_refined_deg 1.546 r_mcbond_it 0.982 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling