☰ Navigation Tabs
Crystal structure of AsDMS D333N mutant in complex with drimenyl phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROFLUIDIC 293 1.72 M ammonium sulfate, 0.095 M MES-NaOH pH6.5, 0.005 M MES-NaOH pH7.0
Crystal Properties Matthews coefficient Solvent content 3.97 69.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.437 α = 90 b = 97.437 β = 90 c = 403.197 γ = 90
Symmetry Space Group P 43 21 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 EIGER X 4M 2023-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.030000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.9 48.37 99.93 0.997 11.77 13.2 44369 71.8384387996
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 2.9 3.004 99.98 0.551 1.16 13.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 2.9000384384 48.3667021781 1.35407072819 44356 2259 99.9707002637 0.203722053666 0.201551739575 0.242734687487 0.2171 67.6794003656
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 17.5872135404 f_angle_d 0.422991461701 f_chiral_restr 0.0378748532206 f_plane_restr 0.00264582703916 f_bond_d 0.00185634117398
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8353 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 151
Software Software Software Name Purpose XDS data reduction XDS data scaling pointless data scaling Aimless data scaling PHASER phasing Coot model building REFMAC refinement PHENIX refinement