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Uba1 in complex with Ub-MLN7243 covalent adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.476 α = 90 b = 193.92 β = 90 c = 230.219 γ = 90
Symmetry Space Group P 2 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 PILATUS3 6M 2015-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.68 20 99 0.13 0.992 10.5 4.5 91638
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 2.68 0.887
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 4NNJ 2.68 20 86846 4499 98.97 0.17375 0.17117 0.1773 0.22398 0.226 RANDOM 49.723
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] -0.94 2.93 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.58 r_dihedral_angle_4_deg 23.104 r_dihedral_angle_3_deg 17.736 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 5.503 r_long_range_B_other 5.486 r_scangle_other 3.152 r_mcangle_it 2.511 r_mcangle_other 2.508 r_angle_refined_deg 1.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.58 r_dihedral_angle_4_deg 23.104 r_dihedral_angle_3_deg 17.736 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 5.503 r_long_range_B_other 5.486 r_scangle_other 3.152 r_mcangle_it 2.511 r_mcangle_other 2.508 r_angle_refined_deg 1.973 r_scbond_it 1.884 r_scbond_other 1.884 r_mcbond_it 1.491 r_mcbond_other 1.49 r_angle_other_deg 1.068 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 17066 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing