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Crystal structure of the UAF1/WDR20/USP12 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K16 5K16, 5K19 and 5K1A experimental model PDB 5K19 5K16, 5K19 and 5K1A experimental model PDB 5K1A 5K16, 5K19 and 5K1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 0.1 M MES, 1.3 M ammonium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 4.58 73.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.903 α = 90 b = 217.903 β = 90 c = 223.819 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 CCD ADSC QUANTUM 315r 2015-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3 50.01 97.8 0.105 0.109 27.4 11.3 58534
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 3 3.05 98.7 1.5 9.2
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 5K16, 5K19 and 5K1A 3 50.01 58534 3014 97.69 0.23239 0.23038 0.2375 0.27083 0.2758 RANDOM 97.881
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] -0.17 -0.09 -0.17 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_4_deg 16.421 r_long_range_B_refined 15.64 r_long_range_B_other 15.639 r_scangle_other 11.188 r_mcangle_it 10.259 r_mcangle_other 10.258 r_dihedral_angle_1_deg 8.651 r_scbond_it 7.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_4_deg 16.421 r_long_range_B_refined 15.64 r_long_range_B_other 15.639 r_scangle_other 11.188 r_mcangle_it 10.259 r_mcangle_other 10.258 r_dihedral_angle_1_deg 8.651 r_scbond_it 7.166 r_scbond_other 7.165 r_mcbond_it 6.633 r_mcbond_other 6.63 r_angle_other_deg 3.832 r_angle_refined_deg 1.737 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 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 9541 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing HKL-2000 data reduction HKL-2000 data scaling