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Vc1313-LBD bound to D-arginine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 293 0.1 M Tris (base) bicine pH 8.6 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000.Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-arginine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000.
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.499 α = 75.81 b = 44.557 β = 84.49 c = 55.337 γ = 74.74
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 X 2M 2021-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 1.9 37.12 96.32 0.0864 0.1031 0.0554 0.994 7.46 3.4 26099 35.43
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 1.9 1.968 0.58
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R-VALUE 1.9 37.12 1.98 26087 96.32 0.1914 0.2062 0.2245 0.2359 42.95
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 4.9578 f_angle_d 0.9555 f_chiral_restr 0.0422 f_plane_restr 0.0084 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Arcimboldo phasing PHASER phasing Coot model building XDS data reduction XDS data scaling