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Ubiquitin binding variants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S1Z 4s1z, 4YII chain A experimental model PDB 4YII 4s1z, 4YII chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 0.1M HEPES pH 7.7, 27.5% PEG3350, 2.5mM APC2 WHB (735-C) + 2.08mM Ubiquitin protein co-mixed
Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.893 α = 90 b = 63.368 β = 90 c = 100.135 γ = 90
Symmetry Space Group P 21 21 21
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 2015-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 2.2 53.55 96.5 0.069 0.069 0.036 12 4.4 17815 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99 0.583 0.583 0.303 4.4
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 4s1z, 4YII chain A 2.2 53.55 17815 980 95.64 0.22287 0.2205 0.2252 0.2662 0.27 RANDOM 48.829
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] -3.75 1.17 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 15.457 r_dihedral_angle_4_deg 13.741 r_long_range_B_refined 7.585 r_long_range_B_other 7.561 r_scangle_other 6.109 r_dihedral_angle_1_deg 5.924 r_mcangle_it 3.998 r_mcangle_other 3.997 r_scbond_it 3.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.842 r_dihedral_angle_3_deg 15.457 r_dihedral_angle_4_deg 13.741 r_long_range_B_refined 7.585 r_long_range_B_other 7.561 r_scangle_other 6.109 r_dihedral_angle_1_deg 5.924 r_mcangle_it 3.998 r_mcangle_other 3.997 r_scbond_it 3.757 r_scbond_other 3.756 r_mcbond_it 2.708 r_mcbond_other 2.708 r_angle_refined_deg 1.34 r_angle_other_deg 0.898 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2395 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing