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Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 291 0.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.16 α = 90 b = 75.16 β = 90 c = 273.77 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 16M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.7 45.67 99.7 0.167 0.997 10.2 6.3 13514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 0.502
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 5cem 2.7 45.67 11150 1021 90.59 0.20676 0.20187 0.2111 0.25967 0.267 RANDOM 58.447
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] -0.25 -0.13 -0.25 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_long_range_B_other 12.697 r_long_range_B_refined 12.69 r_dihedral_angle_3_deg 12.164 r_dihedral_angle_4_deg 10.467 r_scangle_other 8.863 r_mcangle_it 8.391 r_mcangle_other 8.39 r_scbond_it 5.626 r_scbond_other 5.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.472 r_long_range_B_other 12.697 r_long_range_B_refined 12.69 r_dihedral_angle_3_deg 12.164 r_dihedral_angle_4_deg 10.467 r_scangle_other 8.863 r_mcangle_it 8.391 r_mcangle_other 8.39 r_scbond_it 5.626 r_scbond_other 5.624 r_mcbond_it 5.375 r_mcbond_other 5.354 r_dihedral_angle_1_deg 4.889 r_angle_refined_deg 0.955 r_angle_other_deg 0.902 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing