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Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline 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 0.4M SODIUM ACETATE,13%(V/V)PEG 3500, 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 = 185.106 α = 90 b = 51.711 β = 100.11 c = 172.782 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 2.25 40 100 0.09 18 4.5 77267
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 2.25 2.33 100 0.47 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 2.25 169.03 73055 3870 99.6 0.223 0.22 0.2208 0.284 RANDOM 30.56
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] 0.08 -1.79 -1.17 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 16.627 r_dihedral_angle_1_deg 10.995 r_scangle_it 2.882 r_scbond_it 1.932 r_angle_refined_deg 1.588 r_mcangle_it 1.345 r_mcbond_it 0.788 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_dihedral_angle_4_deg 18.021 r_dihedral_angle_3_deg 16.627 r_dihedral_angle_1_deg 10.995 r_scangle_it 2.882 r_scbond_it 1.932 r_angle_refined_deg 1.588 r_mcangle_it 1.345 r_mcbond_it 0.788 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.23 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.118 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 9457 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing