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Human OGT in complex with UDP and fused substrate peptide (HCF1)
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 291 1.3M Ammonium tartrate diabasic; 0.1M Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 3.98 69.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.024 α = 90 b = 168.024 β = 90 c = 162.265 γ = 120
Symmetry Space Group P 62 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 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) R Sym 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 1.9 48.53 100 0.147 0.12 0.998 14.4 20 106157
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 1.9 1.97 99.7 1.95 0.684 1.7 20.2
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 3PE4 1.9 48.5 95998 5042 99.94 0.17094 0.16943 0.18 0.19933 0.2072 RANDOM 30.491
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] -0.35 -0.17 -0.35 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 13.68 r_long_range_B_refined 7.894 r_long_range_B_other 7.894 r_scangle_other 6.218 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.294 r_scbond_other 4.275 r_mcangle_it 3.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_4_deg 19.371 r_dihedral_angle_3_deg 13.68 r_long_range_B_refined 7.894 r_long_range_B_other 7.894 r_scangle_other 6.218 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.294 r_scbond_other 4.275 r_mcangle_it 3.802 r_mcangle_other 3.802 r_mcbond_it 2.803 r_mcbond_other 2.8 r_angle_refined_deg 1.999 r_angle_other_deg 1.069 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 5593 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing