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Crystal Structure of DMATS1 prenyltransferase in complex with L-Tyr and DMSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 294 7.5 mg/mL protein, 0.1 M Tris-HCl (pH 8.9), 0.6 M NaCl, 23% (v/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.27 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.066 α = 90 b = 107.717 β = 90 c = 180.722 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2021-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 107.7 99.8 0.086 0.036 0.999 13.2 6.6 57998 66.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.62 100 1.339 0.597 0.565 1.4
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 Alphafold 2.55 92.53 1.33 57904 2000 99.32 0.2162 0.215 0.2227 0.2506 0.2616 80.27
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 20.2379 f_angle_d 0.7802 f_chiral_restr 0.0503 f_plane_restr 0.0054 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11531 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 27
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building