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Crystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JXM Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 1% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.446 α = 90 b = 129.446 β = 90 c = 49.777 γ = 90
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 EIGER X 16M 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97932 NSLS-II 17-ID-2
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 1.33 29.12 99.8 0.07 0.075 0.027 0.999 15 7.5 95021 13.86
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 1.33 1.36 97.3 0.685 0.739 0.275 0.806 7
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 THROUGHOUT Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing. 1.33 29.118 1.36 95019 1993 99.81 0.1665 0.1662 0.1663 0.1809 0.1814 18.9029
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 2772 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 66
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing