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Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ECB PDB entry 6ECB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 1.65 M DL-malic acid, pH 8.0, 25 mM HEPES, pH 8.0, 100 mM sodium chloride, 0.2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 4.42 72.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.298 α = 90 b = 152.298 β = 90 c = 152.298 γ = 90
Symmetry Space Group P 4 3 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 PIXEL DECTRIS PILATUS 6M-F 2017-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C .9792 APS 24-ID-C
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 1.9 107.69 100 0.123 0.124 0.02 1 23.3 37.2 48063 37.63
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 1.9 1.94
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6ECB 1.9 107.69 1.34 48054 2658 99.98 0.1895 0.1881 0.2012 0.2141 0.2236 59.42
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 11.3396 f_angle_d 1.4015 f_chiral_restr 0.0923 f_bond_d 0.017 f_plane_restr 0.0104
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1786 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing