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Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 25 % P3350, 0.2 M Mg Cl, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.85 33.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.351 α = 90 b = 33.492 β = 90 c = 66.081 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 EIGER2 X 16M 2022-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.4 50 97.9 0.128 0.134 0.039 0.998 7.9 12.2 13611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 78.2 0.724 0.843 0.407 0.126 4.5
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 (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 1.4 33.04 12941 630 97.47 0.16416 0.16196 0.1719 0.20764 0.2149 RANDOM 20.478
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] 0.23 0.3 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.174 r_long_range_B_refined 13.444 r_long_range_B_other 12.889 r_scangle_other 9.402 r_mcangle_other 7.792 r_mcangle_it 7.786 r_dihedral_angle_1_deg 6.52 r_dihedral_angle_2_deg 6.502 r_scbond_it 6.345 r_scbond_other 6.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.174 r_long_range_B_refined 13.444 r_long_range_B_other 12.889 r_scangle_other 9.402 r_mcangle_other 7.792 r_mcangle_it 7.786 r_dihedral_angle_1_deg 6.52 r_dihedral_angle_2_deg 6.502 r_scbond_it 6.345 r_scbond_other 6.336 r_mcbond_it 5.321 r_mcbond_other 5.232 r_rigid_bond_restr 3.346 r_angle_refined_deg 1.356 r_angle_other_deg 0.514 r_chiral_restr 0.079 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 595 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing