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OTUB2 in covalent complex with LN5P45
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5QIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 %v/v 2-Propanol
13 %w/v PEG 4K
0.1 M HEPES pH 8
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.65 α = 90 b = 45.25 β = 96.05 c = 58 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 PIXEL DECTRIS EIGER2 XE 9M 2020-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.77 47.43 99.6 0.118 0.142 0.077 0.994 7 3.2 24095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 99.6 1.295 0.985 0.338 0.7 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.77 47.43 24082 1229 99.591 0.212 0.2099 0.2188 0.2521 0.251 25.72
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] 0.805 -0.657 -0.279 -0.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.263 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 16.396 r_dihedral_angle_other_3_deg 8.61 r_dihedral_angle_1_deg 6.988 r_lrange_other 6.633 r_lrange_it 6.628 r_scangle_it 5.37 r_scangle_other 5.368 r_scbond_it 3.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.263 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 16.396 r_dihedral_angle_other_3_deg 8.61 r_dihedral_angle_1_deg 6.988 r_lrange_other 6.633 r_lrange_it 6.628 r_scangle_it 5.37 r_scangle_other 5.368 r_scbond_it 3.399 r_scbond_other 3.398 r_mcangle_it 3.186 r_mcangle_other 3.18 r_mcbond_it 2.12 r_mcbond_other 2.103 r_angle_refined_deg 1.654 r_angle_other_deg 1.408 r_symmetry_nbd_refined 0.373 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.218 r_nbd_other 0.215 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_other 0.123 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1857 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing