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Structure of a mycobacterium tuberculosis puromycin-hydrolyzing peptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287.15 0.1 M BIS-TRIS propane pH 7, 2.4 M DL-Malic acid pH 7.0 20 % (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.87 74.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.95 α = 90 b = 183.95 β = 90 c = 146.31 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS3 X CdTe 1M 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 46.4897392546 99.9 0.2407 0.2473 0.0564 0.996 7.97 19.5 56249 111.913128818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.107 100 3.358 3.448 0.7807 0.297 0.86 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3AZO 3.00004456732 46.4897392546 1.35974463903 56235 2004 99.9306962363 0.178582720641 0.17714709451 0.1812 0.218114150504 0.2172 0.05 134.932464909
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.2415411243 f_angle_d 1.22176225122 f_chiral_restr 0.0644565888372 f_plane_restr 0.00848852292959 f_bond_d 0.00792193339951
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10055 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling BALBES phasing