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Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a imidazole-pugnac hybrid inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CHO PDB ENTRY 2CHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.6M SODIUM ACETATE,13% (V/V) PEG3500, 0.1M MES PH6.0, 10% (V/V) GLYCEROL, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.426 α = 90 b = 51.34 β = 100.22 c = 85.474 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.97 50 100 0.08 17 4.5 53713
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 1.97 2.04 99 0.49 3 4.4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CHO 1.98 92.85 53713 2870 99.4 0.193 0.192 0.194 0.229 RANDOM 26.14
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] -0.02 -1.38 -0.37 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.937 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 13.941 r_dihedral_angle_1_deg 8.587 r_scangle_it 3.955 r_scbond_it 2.632 r_mcangle_it 1.608 r_angle_refined_deg 1.482 r_mcbond_it 1.03 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.937 r_dihedral_angle_4_deg 16.969 r_dihedral_angle_3_deg 13.941 r_dihedral_angle_1_deg 8.587 r_scangle_it 3.955 r_scbond_it 2.632 r_mcangle_it 1.608 r_angle_refined_deg 1.482 r_mcbond_it 1.03 r_nbtor_refined 0.307 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing