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Unliganded Crystal Structure of Recombinant GBA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Mg formate, 19% (v/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.451 α = 86.04 b = 46.176 β = 75.191 c = 64.209 γ = 82.782
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 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 0.98 31.68 74.2 0.043 0.037 0.994 8.7 1.9 208682
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 0.98 1 0.486 0.486 0.685
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 2NT1 0.98 31.68 208659 9829 74.235 0.112 0.1116 0.1392 0.1282 0.1513 9.105
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] 0.239 0.025 -0.249 0.065 -0.348 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 6.998 r_lrange_it 2.461 r_lrange_other 2.405 r_angle_refined_deg 1.568 r_angle_other_deg 1.513 r_scangle_it 1.154 r_scangle_other 1.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.052 r_dihedral_angle_4_deg 18.453 r_dihedral_angle_3_deg 12.571 r_dihedral_angle_1_deg 6.998 r_lrange_it 2.461 r_lrange_other 2.405 r_angle_refined_deg 1.568 r_angle_other_deg 1.513 r_scangle_it 1.154 r_scangle_other 1.154 r_rigid_bond_restr 0.995 r_mcangle_it 0.937 r_mcangle_other 0.937 r_scbond_it 0.926 r_scbond_other 0.926 r_mcbond_it 0.663 r_mcbond_other 0.663 r_nbd_refined 0.266 r_symmetry_xyhbond_nbd_other 0.254 r_nbd_other 0.241 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.169 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.041 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing