☰ Navigation Tabs
Structure of recombinant human beta-glucocerebrosidase in complex with D-carbaxylosyl chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TN1 6TN1
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 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.277 α = 90 b = 76.465 β = 102.047 c = 68.469 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 2020-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
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 1.58 52.158 100 0.143 0.998 8.8 6.7 73542
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 1.58 1.61 1.569 0.563 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6TN1 1.58 52.158 73507 3644 99.929 0.153 0.1515 0.1517 0.1849 0.185 19.369
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] 0.979 0.81 0.23 -1.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 7.422 r_lrange_it 5.179 r_lrange_other 5.178 r_scangle_it 2.814 r_scangle_other 2.814 r_scbond_it 1.913 r_scbond_other 1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.482 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 13.163 r_dihedral_angle_1_deg 7.422 r_lrange_it 5.179 r_lrange_other 5.178 r_scangle_it 2.814 r_scangle_other 2.814 r_scbond_it 1.913 r_scbond_other 1.912 r_mcangle_it 1.717 r_mcangle_other 1.717 r_angle_refined_deg 1.551 r_angle_other_deg 1.392 r_mcbond_it 1.171 r_mcbond_other 1.17 r_nbd_refined 0.214 r_nbd_other 0.195 r_symmetry_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.183 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.156 r_metal_ion_refined 0.11 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.078 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3926 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing