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Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group H3
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 1.3 M DL-malic acid, pH 8.1, 25 mM HEPES, pH 8.0, 100 mM sodium chloride, 0.2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.04 39.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.571 α = 90 b = 77.571 β = 90 c = 235.151 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 100 PIXEL DECTRIS PILATUS3 S 6M 2018-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 .9794 CLSI 08ID-1
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 2 64.59 100 0.079 0.088 0.053 0.998 9.8 5 35685 39.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.382
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 2 64.59 2.09 35678 1784 99.99 0.2109 0.2092 0.2097 0.2428 0.2429 52.5
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 10.0073 f_angle_d 0.5273 f_chiral_restr 0.0404 f_bond_d 0.0031 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3624 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing