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Lysosomal glucocerebrosidase in complex with a stabilizing nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J25 experimental model PDB 7A17 ChainB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.6 M Magnesium sulfate heptahydrate, 0.1 M MES pH6.5
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.209 α = 90 b = 113.209 β = 90 c = 257.373 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 100 PIXEL DECTRIS EIGER X 9M 2021-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 1.7 46.86 84.9 0.998 13.4 17.1 78278 15.88
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 1.7 1.78 0.52
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 1.7 46.86 1.34 78272 3902 85.31 0.1645 0.1629 0.1632 0.1944 0.1948 20.88
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 6.3946 f_angle_d 0.9621 f_chiral_restr 0.0574 f_plane_restr 0.0088 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4942 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction Aimless data scaling PHENIX phasing