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Structure of recombinant human beta-glucocerebrosidase in complex with galacto-configured cyclophellitol aziridine 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 291 1 M (NH3)2SO4, 0.17 M guanidine HCl, 0.02 M KCl, 0.1 M sodium acetate pH 4.8
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.556 α = 90 b = 285.273 β = 90 c = 91.83 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 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979500 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 1.8 72.197 100 0.116 0.052 0.998 10.9 5.9 134042
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 1.8 1.83 100 1.364 0.848 0.59 1.2 5.8
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 1.8 72.197 134017 6677 99.884 0.177 0.1755 0.183 0.2032 0.2111 28.029
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] 3.874 -1.618 -2.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.299 r_lrange_other 6.299 r_scangle_it 4.219 r_scangle_other 4.219 r_mcangle_it 2.914 r_mcangle_other 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.405 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.299 r_lrange_other 6.299 r_scangle_it 4.219 r_scangle_other 4.219 r_mcangle_it 2.914 r_mcangle_other 2.914 r_scbond_it 2.638 r_scbond_other 2.638 r_mcbond_it 1.871 r_mcbond_other 1.87 r_dihedral_angle_other_1_deg 1.632 r_angle_refined_deg 1.443 r_angle_other_deg 1.295 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.204 r_nbd_other 0.201 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.026 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 7791 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing