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Human OGT in complex with UDP and fused substrate peptide (Tab1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 3.5M sodium formate, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.22 61.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.533 α = 90 b = 98.533 β = 90 c = 367.2 γ = 120
Symmetry Space Group P 61 2 2
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 PILATUS3 S 6M Toroidal mirror 2015-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 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 2.54 49.7 99.8 0.13 16.8 19.2 36043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.63
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 3pe4 2.54 49.7 34136 1795 99.77 0.19599 0.19331 0.2077 0.24466 0.2428 RANDOM 72.052
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] 2.43 1.22 2.43 -7.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.753 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 16.78 r_long_range_B_other 10.245 r_long_range_B_refined 10.244 r_scangle_other 8.146 r_mcangle_it 7.253 r_mcangle_other 7.253 r_dihedral_angle_1_deg 6.675 r_scbond_it 5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.753 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 16.78 r_long_range_B_other 10.245 r_long_range_B_refined 10.244 r_scangle_other 8.146 r_mcangle_it 7.253 r_mcangle_other 7.253 r_dihedral_angle_1_deg 6.675 r_scbond_it 5.65 r_scbond_other 5.649 r_mcbond_it 5.026 r_mcbond_other 5.026 r_angle_refined_deg 1.783 r_angle_other_deg 1.052 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5664 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing