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Crystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from Chlamydia trachomatis D/UW-3/Cx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 ChtrB.00799.a.B1.PW38523 at 16.07 mg/mL with 2 mM L-Leucine set up against MCSG3 screen condition C8: 0.1 M Tris pH 8.5, 3.2 M NaCl; supplemented with 20% ethylene glycol as cryo-protectant; unique puck ID ejv5-2, crystal tracking ID 305504c8
Crystal Properties Matthews coefficient Solvent content 3.18 61.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.96 α = 90 b = 137.96 β = 90 c = 128.14 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.95 45.158 100 0.065 0.067 1 27.75 14.566 52788 35.256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.57 0.591 0.95 5.27 14.82
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4zi6 1.95 45.158 51435 3108 97.43 0.1444 0.1427 0.1448 0.1714 0.174 37.8511
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3731 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction