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Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY Tagged Cyclophellitol activity based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.956 α = 90 b = 158.42 β = 102.147 c = 68.238 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.86 158.42 100 0.119 0.129 0.996 9.1 6.9 91928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 0.843 0.913 0.859 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6TJK 1.86 66.8 91876 4665 99.94 0.18 0.1769 0.1782 0.2318 0.2342 24.294
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] 0.347 0.087 1.848 -2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 37.453 r_dihedral_angle_2_deg 34.286 r_dihedral_angle_4_deg 20.072 r_dihedral_angle_3_deg 14.196 r_dihedral_angle_1_deg 7.478 r_lrange_it 4.949 r_lrange_other 4.949 r_scangle_it 3.437 r_scangle_other 3.437 r_scbond_it 2.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 37.453 r_dihedral_angle_2_deg 34.286 r_dihedral_angle_4_deg 20.072 r_dihedral_angle_3_deg 14.196 r_dihedral_angle_1_deg 7.478 r_lrange_it 4.949 r_lrange_other 4.949 r_scangle_it 3.437 r_scangle_other 3.437 r_scbond_it 2.404 r_scbond_other 2.403 r_mcangle_it 2.356 r_mcangle_other 2.355 r_mcbond_it 1.722 r_mcbond_other 1.722 r_angle_refined_deg 1.57 r_angle_other_deg 1.329 r_nbd_other 0.24 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.08 r_symmetry_xyhbond_nbd_other 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7819 Nucleic Acid Atoms Solvent Atoms 744 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing