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Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ADP
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 7.5 291 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350, 0.1 M Sodium Hepes, MOPS pH 7.5, 0.09 M Sodium nitrate, 0.09 M Sodium phosphate dibasic, 0.09 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.87 34.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.371 α = 90 b = 33.671 β = 90 c = 66.421 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 2022-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.17 50 98.3 0.052 0.057 0.022 0.999 11.5 6.6 23321
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 1.17 1.19 83 0.214 0.251 0.129 0.927 3.3
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 1.17 30.05 22138 1134 98.24 0.15089 0.14978 0.1583 0.17251 0.176 RANDOM 11.591
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] 1.33 -0.61 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.765 r_long_range_B_refined 12.506 r_long_range_B_other 11.484 r_dihedral_angle_1_deg 6.434 r_scangle_other 6.082 r_dihedral_angle_2_deg 5.88 r_mcangle_it 5.038 r_mcangle_other 5.037 r_scbond_it 3.96 r_scbond_other 3.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.765 r_long_range_B_refined 12.506 r_long_range_B_other 11.484 r_dihedral_angle_1_deg 6.434 r_scangle_other 6.082 r_dihedral_angle_2_deg 5.88 r_mcangle_it 5.038 r_mcangle_other 5.037 r_scbond_it 3.96 r_scbond_other 3.959 r_mcbond_it 3.275 r_mcbond_other 3.262 r_rigid_bond_restr 3.145 r_angle_refined_deg 1.495 r_angle_other_deg 0.597 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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 590 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing