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Crystal structure of recombinant human beta-glucocerebrosidase in complex with adamantyl-cyclophellitol inhibitor (ME656)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Ammonium sulfate, Guanidine Hydrochloride, Potassium Chloride, Sodium Acetate (pH 4.6)
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.214 α = 90 b = 285.131 β = 90 c = 92.003 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS3 6M 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.977180 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.81 72.08 99.95 0.132 7.71 6.53 131678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.84 1.02
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NT0 1.81 72.08 125104 6547 99.89 0.17804 0.1764 0.20977 0.2011 RANDOM 27.68
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] 3.28 -0.98 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 7.593 r_long_range_B_other 6.491 r_long_range_B_refined 6.49 r_scangle_other 4.735 r_scbond_it 3.176 r_scbond_other 3.176 r_mcangle_other 3.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 7.593 r_long_range_B_other 6.491 r_long_range_B_refined 6.49 r_scangle_other 4.735 r_scbond_it 3.176 r_scbond_other 3.176 r_mcangle_other 3.079 r_mcangle_it 3.078 r_mcbond_it 2.245 r_mcbond_other 2.165 r_angle_refined_deg 1.627 r_angle_other_deg 1.365 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7830 Nucleic Acid Atoms Solvent Atoms 936 Heterogen Atoms 334
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing