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Structure of recombinant human beta-glucocerebrosidase in complex with azide tagged cyclophellitol epoxide inhibitor
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 4.6 291 1 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 3.2 61.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.89 α = 90 b = 285.769 β = 90 c = 91.674 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 X 16M 2016-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979490 Diamond I02
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 68.202 99.9 0.077 0.036 0.999 12.1 5.5 156446
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 1.614 0.741 0.538 1.1 5.7
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 68.202 156420 7842 99.861 0.187 0.1859 0.2077 0.2121 0.2343 31.556
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] 4.941 -2.094 -2.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_other_1_deg 30.789 r_dihedral_angle_4_deg 19.613 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.293 r_lrange_other 6.01 r_lrange_it 6.009 r_scangle_it 4.009 r_scangle_other 4.009 r_mcangle_it 2.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_other_1_deg 30.789 r_dihedral_angle_4_deg 19.613 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_1_deg 7.293 r_lrange_other 6.01 r_lrange_it 6.009 r_scangle_it 4.009 r_scangle_other 4.009 r_mcangle_it 2.989 r_mcangle_other 2.989 r_scbond_other 2.57 r_scbond_it 2.569 r_mcbond_it 1.976 r_mcbond_other 1.975 r_angle_refined_deg 1.428 r_angle_other_deg 1.279 r_nbd_refined 0.206 r_symmetry_nbd_other 0.179 r_nbd_other 0.178 r_symmetry_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 661 Heterogen Atoms 277
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing