☰ Navigation Tabs
Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl fluoride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AWK 8AWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.92 α = 90 b = 155.984 β = 101.964 c = 68.036 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 2020-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976230 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.59 51.99 99.6 0.135 0.997 8.6 6.9 994940
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.62 1.8 0.544 1.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8AWK 1.59 51.824 143489 7124 99.434 0.183 0.1819 0.2125 0.1964 20.388
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] 1.471 0.406 -0.003 -1.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 40.093 r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.453 r_lrange_it 4.281 r_lrange_other 4.135 r_scangle_it 2.325 r_scangle_other 2.325 r_mcangle_it 1.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_1_deg 40.093 r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 13.142 r_dihedral_angle_1_deg 7.453 r_lrange_it 4.281 r_lrange_other 4.135 r_scangle_it 2.325 r_scangle_other 2.325 r_mcangle_it 1.693 r_mcangle_other 1.693 r_scbond_it 1.557 r_scbond_other 1.557 r_angle_refined_deg 1.417 r_angle_other_deg 1.302 r_mcbond_it 1.138 r_mcbond_other 1.137 r_nbd_other 0.232 r_metal_ion_refined 0.205 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.167 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.074 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 7845 Nucleic Acid Atoms Solvent Atoms 893 Heterogen Atoms 400
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing