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CpOGA D298N in complex with TAB1-derived O-GlcNAc peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J62 PDB ENTRY 2J62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.5 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.09 α = 90 b = 118.09 β = 90 c = 148.26 γ = 120
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 2010-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.55 25 99 0.12 7.1 3.1 37698 2
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 PDB ENTRY 2J62 2.55 25 36914 777 98.84 0.20087 0.20007 0.1993 0.23846 0.233 RANDOM 36.495
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] 2.14 1.07 2.14 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.291 r_dihedral_angle_4_deg 15.732 r_sphericity_free 15.312 r_dihedral_angle_3_deg 15.105 r_dihedral_angle_1_deg 6.16 r_scangle_it 4.084 r_scbond_it 2.287 r_angle_refined_deg 1.404 r_mcangle_it 1.207 r_mcbond_it 0.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.291 r_dihedral_angle_4_deg 15.732 r_sphericity_free 15.312 r_dihedral_angle_3_deg 15.105 r_dihedral_angle_1_deg 6.16 r_scangle_it 4.084 r_scbond_it 2.287 r_angle_refined_deg 1.404 r_mcangle_it 1.207 r_mcbond_it 0.539 r_chiral_restr 0.093 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_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_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_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4614 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing