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Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl chloride
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, 0.25M HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.43 49.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.111 α = 90 b = 76.48 β = 101.957 c = 68.147 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 1.49 51.96 98.9 0.104 0.997 8.6 6.7 85933
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 1.49 1.52 1.673 0.608 0.9
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 8AWK 1.49 51.96 85814 4206 98.616 0.185 0.1834 0.185 0.2216 0.224 22.777
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] 1.032 0.667 0.492 -1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_4_deg 17.366 r_dihedral_angle_3_deg 12.864 r_dihedral_angle_1_deg 7.021 r_lrange_it 4.661 r_scangle_it 2.293 r_scbond_it 1.565 r_mcangle_it 1.449 r_angle_refined_deg 1.215 r_mcbond_it 0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_4_deg 17.366 r_dihedral_angle_3_deg 12.864 r_dihedral_angle_1_deg 7.021 r_lrange_it 4.661 r_scangle_it 2.293 r_scbond_it 1.565 r_mcangle_it 1.449 r_angle_refined_deg 1.215 r_mcbond_it 0.972 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.136 r_metal_ion_refined 0.128 r_chiral_restr 0.092 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3922 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing