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Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.139 α = 90 b = 76.67 β = 102.053 c = 67.988 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 XE 16M 2019-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979507 Diamond I04
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 76.67 100 0.207 0.084 0.995 6.7 7 49541
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 1.84 100 2.351 1.301 0.506 0.8 6.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6TJK 1.8 66.578 49519 2509 99.962 0.179 0.1782 0.1894 0.1713 25.448
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] 1.832 1.153 0.507 -2.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.291 r_dihedral_angle_4_deg 19.941 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 7.487 r_lrange_it 3.832 r_lrange_other 3.666 r_scangle_it 2.355 r_scangle_other 2.355 r_mcangle_it 1.634 r_mcangle_other 1.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.291 r_dihedral_angle_4_deg 19.941 r_dihedral_angle_3_deg 13.025 r_dihedral_angle_1_deg 7.487 r_lrange_it 3.832 r_lrange_other 3.666 r_scangle_it 2.355 r_scangle_other 2.355 r_mcangle_it 1.634 r_mcangle_other 1.634 r_scbond_it 1.523 r_scbond_other 1.523 r_angle_refined_deg 1.388 r_angle_other_deg 1.25 r_mcbond_it 1.072 r_mcbond_other 1.069 r_nbd_other 0.234 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.203 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3922 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing