☰ Navigation Tabs
The crystal structure of SAUGI/human UDG complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKZ 1AKZ, 3WDG experimental model PDB 3WDG 1AKZ, 3WDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Tris HCl pH8.5, 0.2 M MgCl2 6H2O and 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.831 α = 90 b = 52.853 β = 112.36 c = 82.338 γ = 90
Symmetry Space Group C 1 2 1
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 QUANTUM 315r 2013-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.97622 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 96.1 14 3.1 26778
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 2.4 2.49 97.7 1.7 3
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 1AKZ, 3WDG 2.4 30.927 25371 1344 95.38 0.16691 0.16527 0.1646 0.19767 0.1947 RANDOM 41.49
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] 2.73 -1.04 -1.14 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.722 r_dihedral_angle_4_deg 20.967 r_dihedral_angle_3_deg 18.621 r_dihedral_angle_1_deg 7.272 r_scangle_it 4.795 r_mcangle_it 3.552 r_scbond_it 3.273 r_mcbond_it 2.119 r_angle_refined_deg 1.463 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.722 r_dihedral_angle_4_deg 20.967 r_dihedral_angle_3_deg 18.621 r_dihedral_angle_1_deg 7.272 r_scangle_it 4.795 r_mcangle_it 3.552 r_scbond_it 3.273 r_mcbond_it 2.119 r_angle_refined_deg 1.463 r_chiral_restr 0.118 r_gen_planes_refined 0.014 r_bond_refined_d 0.009 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_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5480 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Blu-Ice data reduction HKL-2000 data scaling MOLREP phasing