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Structure of recombinant human beta-glucocerebrosidase in complex with BODIPY functionalised epoxide activity based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.95 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.27 62.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.172 α = 90 b = 285.622 β = 90 c = 91.564 γ = 90
Symmetry Space Group C 2 2 21
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 2015-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976300 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 103.82 100 0.09 0.04 0.999 13.3 6 159511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.973 0.445 0.761 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 2NT0 1.7 103.816 159484 7997 99.91 0.163 0.1626 0.1718 0.1805 0.1897 23.297
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] 3.633 -1.26 -2.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.952 r_dihedral_angle_4_deg 19.31 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 7.269 r_lrange_it 4.892 r_lrange_other 4.892 r_dihedral_angle_other_1_deg 3.541 r_scangle_it 2.943 r_scangle_other 2.943 r_mcangle_it 1.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.952 r_dihedral_angle_4_deg 19.31 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 7.269 r_lrange_it 4.892 r_lrange_other 4.892 r_dihedral_angle_other_1_deg 3.541 r_scangle_it 2.943 r_scangle_other 2.943 r_mcangle_it 1.886 r_mcangle_other 1.886 r_scbond_it 1.833 r_scbond_other 1.833 r_angle_refined_deg 1.434 r_angle_other_deg 1.288 r_mcbond_it 1.186 r_mcbond_other 1.185 r_dihedral_angle_other_2_deg 0.803 r_symmetry_nbd_refined 0.202 r_nbd_refined 0.197 r_symmetry_nbd_other 0.174 r_nbd_other 0.168 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.15 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7840 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 331
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing