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O-GlcNAc transferase from Drososphila melanogaster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PE4 PDB ENTRY 3PE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 CONDITION 70 OF THE MOLECULAR DIMENSIONS MORPHEUS SCREEN 0.12 M MIX OF D-GLUCOSE, D-MANNOSE, D-GALACTOSE, L-FUCOSE, D-XYLOSE, N-ACETYL-D-GLUCOSAMINE, 30% PEG8000/ETHYLENE GLYCEROL AND 0.1 M TRIS-BICINE PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.946 α = 90 b = 160.946 β = 90 c = 77.189 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 DECTRIS PILATUS 6M 2014-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.66 35 99.7 0.12 8.8 5.1 63989 2
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 2.66 2.75 99.1 0.92 1.5 4.9
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 3PE4 2.66 35 60715 3238 99.68 0.22672 0.22475 0.2231 0.2638 0.2607 RANDOM 50.263
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] 1.21 0.6 1.21 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.239 r_dihedral_angle_3_deg 19.048 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_1_deg 5.549 r_angle_refined_deg 1.259 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.239 r_dihedral_angle_3_deg 19.048 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_1_deg 5.549 r_angle_refined_deg 1.259 r_chiral_restr 0.085 r_bond_refined_d 0.008 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_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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16026 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing