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Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.1 M bis-tris-propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.744 α = 90 b = 156.222 β = 102.473 c = 68.264 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 X 16M 2019-07-19 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 1.56 66.742 99.4 0.105 0.057 0.987 7.4 4.3 147746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 1.67 0.901 0.336 0.7
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 6Q6K 1.56 66.742 147674 7465 96.714 0.166 0.1646 0.1659 0.1985 0.1996 22.553
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] 1.457 0.66 -0.632 -1.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 7.472 r_lrange_it 4.783 r_lrange_other 4.779 r_scangle_it 3.369 r_scangle_other 3.368 r_scbond_it 2.37 r_scbond_other 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 7.472 r_lrange_it 4.783 r_lrange_other 4.779 r_scangle_it 3.369 r_scangle_other 3.368 r_scbond_it 2.37 r_scbond_other 2.37 r_mcangle_it 2.15 r_mcangle_other 2.15 r_angle_refined_deg 1.588 r_mcbond_it 1.579 r_mcbond_other 1.576 r_angle_other_deg 1.394 r_nbd_other 0.236 r_nbd_refined 0.214 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.181 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.171 r_chiral_restr_other 0.166 r_symmetry_nbd_refined 0.149 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7833 Nucleic Acid Atoms Solvent Atoms 895 Heterogen Atoms 411
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing