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Crystal structure of AsDMS D333N mutant in complex with farnesyl pyrophosphate
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 VAPOR DIFFUSION, SITTING DROP 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 3.88 68.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.546 α = 90 b = 96.546 β = 90 c = 401.409 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 2022-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.040000 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 2.6 49.3031591263 99.95 0.998 13.84 13.5 59769 53.557292161
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 2.6 2.693 100 0.72 1.85 14.2
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 2.60002725624 49.3031591263 1.3523052928 59760 3043 99.9799237101 0.195099463997 0.192910874098 0.204 0.235672843876 0.238 55.7535927991
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 20.8366102478 f_angle_d 0.946843155465 f_chiral_restr 0.0503971462001 f_bond_d 0.00824898753129 f_plane_restr 0.00587704564222
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8397 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 179
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