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ST0452(Y97N)-GlcNAc binding form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% (w/v) PEG3350, 0.2M potassium citrate tribasic monohydrate
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.843 α = 110.62 b = 94.951 β = 101.47 c = 101.906 γ = 113.03
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 2.09 87.8 96.9 0.072 22 3.6 154041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.15 0.415
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 2GGO 2.09 87.79 146187 7863 96.49 0.19481 0.1929 0.1993 0.23154 0.2365 RANDOM 35.968
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.224 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_3_deg 16.485 r_long_range_B_refined 8.533 r_long_range_B_other 8.518 r_dihedral_angle_1_deg 6.963 r_scangle_other 6.8 r_mcangle_it 4.629 r_mcangle_other 4.629 r_scbond_it 4.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.224 r_dihedral_angle_4_deg 21.608 r_dihedral_angle_3_deg 16.485 r_long_range_B_refined 8.533 r_long_range_B_other 8.518 r_dihedral_angle_1_deg 6.963 r_scangle_other 6.8 r_mcangle_it 4.629 r_mcangle_other 4.629 r_scbond_it 4.363 r_scbond_other 4.363 r_mcbond_it 3.248 r_mcbond_other 3.248 r_angle_refined_deg 1.859 r_angle_other_deg 1.513 r_chiral_restr 0.144 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.007 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 18701 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing