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CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 CpOGA D298N was concentrated to 35 mg/ml in 25 mM Tris/HCl (pH 8.0) and crystallized from 0.175 M CdSO4 and 0.6 M sodium acetate pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.6 73.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.56 α = 90 b = 118.56 β = 90 c = 148.441 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 PIXEL PSI PILATUS 6M 2015-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8729 ESRF ID23-1
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 2.6 34.9 99.4 0.152 7.3 3.3 36087
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 2.6 2.72 99 0.862 3.3 4368
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 2yds 2.6 34.9 35353 729 99.26 0.17155 0.17051 0.1697 0.2201 0.2207 RANDOM 42.751
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]
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.638 r_dihedral_angle_2_deg 37.794 r_sphericity_bonded 28.239 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_1_deg 5.12 r_rigid_bond_restr 1.467 r_angle_refined_deg 1.007 r_chiral_restr 0.069 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.638 r_dihedral_angle_2_deg 37.794 r_sphericity_bonded 28.239 r_dihedral_angle_3_deg 13.842 r_dihedral_angle_4_deg 13.452 r_dihedral_angle_1_deg 5.12 r_rigid_bond_restr 1.467 r_angle_refined_deg 1.007 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4601 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing