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Crystal structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol activity based probe with Cy5 tag (ME569)
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, Gaunidine Hydrochloride, Potassium chloride and Sodium acetate (pH 4.6)
Crystal Properties Matthews coefficient Solvent content 3.28 62.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.613 α = 90 b = 285.934 β = 90 c = 92.258 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 PILATUS 6M-F 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915870 Diamond I04-1
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 1.92 77.64 100 0.19 5.9 8.4 111507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 99.9 0.707 1.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NT0 1.92 77.64 105810 5680 99.95 0.18685 0.185 0.202 0.22101 0.237 RANDOM 37.55
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] 5.85 -1.77 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.921 r_dihedral_angle_4_deg 18.809 r_dihedral_angle_3_deg 14.775 r_long_range_B_refined 7.641 r_long_range_B_other 7.641 r_dihedral_angle_1_deg 7.619 r_scangle_other 5.478 r_mcangle_other 4.294 r_mcangle_it 4.293 r_scbond_it 3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.921 r_dihedral_angle_4_deg 18.809 r_dihedral_angle_3_deg 14.775 r_long_range_B_refined 7.641 r_long_range_B_other 7.641 r_dihedral_angle_1_deg 7.619 r_scangle_other 5.478 r_mcangle_other 4.294 r_mcangle_it 4.293 r_scbond_it 3.64 r_scbond_other 3.64 r_mcbond_it 2.944 r_mcbond_other 2.923 r_angle_refined_deg 1.603 r_angle_other_deg 1.298 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 7764 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 354
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing