☰ Navigation Tabs
Crystal of Glucosidase form Ophiorrhiza pumila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 Consistent with the conditions under which loganin was added, the reservoir solution consisted of 0.1 M sodium acetate trihydrate at pH 4.6 and 2.0 M ammonium sulfate. The sessile drop plate was covered with an adhesive tape and incubated in a cabinet maintained at a temperature of 291.15 K. Diffraction-quality crystals were produced within a time-frame of 10 to 15 days.
Crystal Properties Matthews coefficient Solvent content 3.18 61.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.755 α = 90 b = 137.755 β = 90 c = 164.896 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277.15 PIXEL DECTRIS PILATUS 6M 2024-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97923 SSRF BL19U1
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 1.949 62.93 99.19 0.999 14.36 1.993 57388 27.2
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 1.949 2.019 0.849
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-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 1.95 62.93 1.34 57360 1998 99.2 0.1799 0.1791 0.1799 0.203 0.2041 26.87
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 6.8864 f_angle_d 0.941 f_chiral_restr 0.0582 f_plane_restr 0.0093 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3779 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement autoPX data reduction Aimless data scaling PHENIX phasing