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Crystal Structure of Recombinant GBA in Complex with 2-Deoxy-2-fluoro-beta-D-glucopyranoside
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 293 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.112 α = 90 b = 76.351 β = 101.987 c = 68.16 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 0.9795 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 1.41 51.95 100 0.135 0.056 0.999 7.2 6.7 102363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 7.72 2.388 0.357 0.4
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 6TJK 1.41 51.95 102326 4992 99.9 0.179 0.1776 0.1815 0.2053 0.2088 20.829
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] 0.462 0.748 1.266 -1.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.684 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_1_deg 18.896 r_dihedral_angle_3_deg 13.019 r_lrange_it 4.66 r_lrange_other 4.399 r_scangle_it 2.596 r_scangle_other 2.595 r_scbond_it 1.742 r_scbond_other 1.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.684 r_dihedral_angle_4_deg 20.58 r_dihedral_angle_1_deg 18.896 r_dihedral_angle_3_deg 13.019 r_lrange_it 4.66 r_lrange_other 4.399 r_scangle_it 2.596 r_scangle_other 2.595 r_scbond_it 1.742 r_scbond_other 1.741 r_mcangle_it 1.637 r_mcangle_other 1.637 r_angle_refined_deg 1.461 r_angle_other_deg 1.358 r_mcbond_it 1.136 r_mcbond_other 1.136 r_nbd_other 0.234 r_nbd_refined 0.208 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.164 r_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.096 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3923 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing