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Ube2T in complex with fragment EM04
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 potassium acetate, Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.817 α = 90 b = 55.817 β = 90 c = 185.278 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 6M-F 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 53.45 99.2 14 5.5 12037
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 1YH2 2.4 53.44 11397 629 98.56 0.21192 0.20986 0.2153 0.24734 0.2516 RANDOM 64.201
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] 3.34 3.34 -6.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.973 r_dihedral_angle_4_deg 18.398 r_dihedral_angle_3_deg 12.935 r_long_range_B_refined 8.896 r_long_range_B_other 8.893 r_scangle_other 6.134 r_dihedral_angle_1_deg 5.928 r_mcangle_it 5.489 r_mcangle_other 5.486 r_scbond_it 3.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.973 r_dihedral_angle_4_deg 18.398 r_dihedral_angle_3_deg 12.935 r_long_range_B_refined 8.896 r_long_range_B_other 8.893 r_scangle_other 6.134 r_dihedral_angle_1_deg 5.928 r_mcangle_it 5.489 r_mcangle_other 5.486 r_scbond_it 3.594 r_scbond_other 3.591 r_mcbond_other 3.383 r_mcbond_it 3.381 r_angle_refined_deg 1.312 r_angle_other_deg 0.945 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 1217 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing