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Structure of recombinant human beta-glucocerebrosidase in complex with N-acyl functionalised cyclophellitol aziridine
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, 0.03 M KCl, 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 3.26 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.699 α = 90 b = 285.525 β = 90 c = 91.902 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 2016-01-21 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 1.76 47.633 99.8 0.098 0.042 0.997 10 6.3 143462
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 1.76 1.79 99.9 0.845 0.37 0.835 1.7 6.2
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 1.76 47.633 143436 7160 99.7 0.184 0.183 0.202 0.2084 0.2281 31.049
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] 5.597 -2.895 -2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_4_deg 20.04 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 7.202 r_lrange_it 6.016 r_lrange_other 6.016 r_dihedral_angle_other_1_deg 4.82 r_scangle_it 4.192 r_scangle_other 4.192 r_mcangle_it 2.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_4_deg 20.04 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 7.202 r_lrange_it 6.016 r_lrange_other 6.016 r_dihedral_angle_other_1_deg 4.82 r_scangle_it 4.192 r_scangle_other 4.192 r_mcangle_it 2.913 r_mcangle_other 2.913 r_scbond_it 2.649 r_scbond_other 2.648 r_mcbond_it 1.931 r_mcbond_other 1.931 r_angle_refined_deg 1.447 r_angle_other_deg 1.267 r_nbd_refined 0.202 r_nbd_other 0.185 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.055 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 7808 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 314
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing