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Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis from trigonal partially dehydrated crystal
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 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.47 α = 90 b = 59.47 β = 90 c = 80.42 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 Mirrors 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 3.2 43 0.155 9.9 3.9 2900 32.3
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 3.2 3.37
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 3.2 30 2750 132 98.36 0.23347 0.23172 0.2297 0.2698 0.2708 RANDOM 18.918
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] -1.8 -0.9 -1.8 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.161 r_dihedral_angle_3_deg 22.106 r_dihedral_angle_4_deg 19.992 r_mcangle_it 15.651 r_mcbond_it 11.682 r_dihedral_angle_1_deg 4.679 r_angle_refined_deg 1.526 r_scangle_it 0.489 r_scbond_it 0.435 r_symmetry_hbond_refined 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.161 r_dihedral_angle_3_deg 22.106 r_dihedral_angle_4_deg 19.992 r_mcangle_it 15.651 r_mcbond_it 11.682 r_dihedral_angle_1_deg 4.679 r_angle_refined_deg 1.526 r_scangle_it 0.489 r_scbond_it 0.435 r_symmetry_hbond_refined 0.372 r_symmetry_vdw_refined 0.33 r_nbtor_refined 0.327 r_nbd_refined 0.285 r_xyhbond_nbd_refined 0.209 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1340 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling