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Crystal structure of MYORG (D520N) in complex with Gal-a1,4-Glc
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 7.0, 10% PEG MME5000 and 5% tasimate pH7.0
Crystal Properties Matthews coefficient Solvent content 3.1 60.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.286 α = 80.909 b = 79.099 β = 79.112 c = 178.016 γ = 62.667
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 2021-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
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 2.25 64.53 98.2 0.073 0.103 0.073 0.99 7.9 3.1 161989
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 2.25 2.29 0.8 1.131 0.8 0.962 1 3.1
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 THROUGHOUT 2F2H 2.25 64.53 161977 8099 98.198 0.213 0.2122 0.2175 0.2266 0.231 50.45
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] -0.466 -0.418 2.387 0.442 -0.397 0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.099 r_dihedral_angle_4_deg 18.618 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_1_deg 7.042 r_lrange_it 3.255 r_lrange_other 3.235 r_dihedral_angle_other_1_deg 2.921 r_mcangle_it 1.357 r_mcangle_other 1.357 r_scangle_it 1.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.099 r_dihedral_angle_4_deg 18.618 r_dihedral_angle_3_deg 15.515 r_dihedral_angle_1_deg 7.042 r_lrange_it 3.255 r_lrange_other 3.235 r_dihedral_angle_other_1_deg 2.921 r_mcangle_it 1.357 r_mcangle_other 1.357 r_scangle_it 1.343 r_scangle_other 1.343 r_angle_refined_deg 1.311 r_angle_other_deg 1.111 r_mcbond_it 0.795 r_mcbond_other 0.795 r_scbond_it 0.787 r_scbond_other 0.787 r_nbd_other 0.197 r_nbd_refined 0.177 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.112 r_symmetry_xyhbond_nbd_other 0.106 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.054 r_ncsr_local_group_1 0.054 r_ncsr_local_group_3 0.051 r_ncsr_local_group_5 0.051 r_ncsr_local_group_6 0.047 r_ncsr_local_group_2 0.046 r_ncsr_local_group_4 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19783 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 520
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing