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Catalytic domain of Sst2 F403A mutant bound to ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.139 α = 90 b = 58.174 β = 109.3 c = 56.442 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2014-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 1.719 53.27 99.9 0.047 0.047 23.6 3.8 26060
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 99.9 0.561 2.32 3.6
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 4K1R 1.72 53.27 26060 1382 99.8 0.203 0.201 0.2106 0.237 0.2452 RANDOM 38.31
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.534 r_dihedral_angle_4_deg 14.62 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 5.849 r_long_range_B_other 5.849 r_scangle_other 4.075 r_mcangle_it 2.897 r_mcangle_other 2.896 r_scbond_it 2.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.534 r_dihedral_angle_4_deg 14.62 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 5.849 r_long_range_B_other 5.849 r_scangle_other 4.075 r_mcangle_it 2.897 r_mcangle_other 2.896 r_scbond_it 2.838 r_scbond_other 2.837 r_mcbond_it 2.209 r_mcbond_other 2.208 r_angle_refined_deg 1.896 r_angle_other_deg 0.881 r_chiral_restr 0.114 r_bond_refined_d 0.018 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 2019 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing