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Crystal structure of MYORG bound to 1-deoxygalactonojirimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 100 mM HEPES pH 7.0, 10% PEG MME5000, 5% tasimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.113 α = 80.777 b = 78.882 β = 80.209 c = 176.221 γ = 62.641
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 2020-02-20 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) Rrim I (All) 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 2.43 69.75 98.3 0.073 0.103 0.073 0.995 8.4 3.5 127078
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.47 0.724 1.024 0.724 0.555 1.4 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2F2H 2.43 69.75 126937 6096 98.126 0.225 0.2239 0.2497 0.2447 56.614
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] -2.596 0.001 2.982 0.311 -1.895 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.366 r_dihedral_angle_4_deg 20.098 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_1_deg 7.435 r_lrange_it 4.222 r_lrange_other 4.218 r_mcangle_it 1.804 r_mcangle_other 1.804 r_scangle_it 1.706 r_scangle_other 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.366 r_dihedral_angle_4_deg 20.098 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_1_deg 7.435 r_lrange_it 4.222 r_lrange_other 4.218 r_mcangle_it 1.804 r_mcangle_other 1.804 r_scangle_it 1.706 r_scangle_other 1.706 r_angle_refined_deg 1.428 r_angle_other_deg 1.166 r_mcbond_it 1.1 r_mcbond_other 1.1 r_scbond_it 1.042 r_scbond_other 1.041 r_symmetry_xyhbond_nbd_refined 0.28 r_nbd_other 0.209 r_nbd_refined 0.191 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_other 0.172 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.096 r_ncsr_local_group_5 0.078 r_ncsr_local_group_1 0.076 r_ncsr_local_group_4 0.075 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_2 0.073 r_ncsr_local_group_6 0.071 r_ncsr_local_group_3 0.067 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18863 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 404
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing