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Bacterial O-GlcNAcase (OGA) with compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.5 M NaAcetate, 15% PEG 3350, 0.1 M MES pH 6.0, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.771 α = 90 b = 52.646 β = 99.693 c = 84.464 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 QUANTUM 315r 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 41.63 93.41 0.05266 0.998 17.46 3.6 52607
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.064 58.42 0.4469 0.781 1.6
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 FREE R-VALUE 2CHN 2 41.63 52602 2673 93.432 0.188 0.186 0.1906 0.2183 0.2222 49.748
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] 0.848 -2.838 -1.759 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.952 r_scangle_it 2.52 r_mcangle_it 1.976 r_scbond_it 1.616 r_angle_refined_deg 1.356 r_mcbond_it 1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.602 r_dihedral_angle_3_deg 16.973 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.952 r_scangle_it 2.52 r_mcangle_it 1.976 r_scbond_it 1.616 r_angle_refined_deg 1.356 r_mcbond_it 1.207 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_refined 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4759 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing