☰ Navigation Tabs
Structure of recombinant human beta-glucocerebrosidase in complex with 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, SITTING DROP 291 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.07 59.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.155 α = 90 b = 156.779 β = 102.116 c = 68.23 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 X 16M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9762 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 66.799 99.9 0.159 0.064 0.994 6.3 6.6 119361
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 99.7 1.83 1.07 0.547 1
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 66.799 119361 5927 99.883 0.161 0.1592 0.1599 0.2026 0.2037 24.919
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] 0.659 0.144 0.625 -1.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 48.62 r_dihedral_angle_2_deg 33.948 r_dihedral_angle_4_deg 19.2 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 7.497 r_lrange_it 5.163 r_lrange_other 5.162 r_scangle_it 3.628 r_scangle_other 3.628 r_scbond_it 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 48.62 r_dihedral_angle_2_deg 33.948 r_dihedral_angle_4_deg 19.2 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 7.497 r_lrange_it 5.163 r_lrange_other 5.162 r_scangle_it 3.628 r_scangle_other 3.628 r_scbond_it 2.57 r_scbond_other 2.57 r_mcangle_it 2.301 r_mcangle_other 2.3 r_mcbond_it 1.704 r_mcbond_other 1.704 r_angle_refined_deg 1.591 r_angle_other_deg 1.372 r_nbd_other 0.31 r_symmetry_nbd_refined 0.245 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.209 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.163 r_symmetry_xyhbond_nbd_other 0.108 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7833 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 360
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing