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Transportin-3 TNPO3 in complex with RSY region of CIRBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.5ul Protein (TNPO3) 12mg/ml with 0.2ul Ligand (CIRBP) 4.4mg/ml and 0.1ul seeding stock were mixed with 0.5ul of condition.
Condition: 0.1M Sodium HEPES, 0.1M MOPS (acid), 7.5pH, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.05% w/v D-Salicin, 0.05% w/v Esculin hydrate, 0.05% w/v Quinine hemisulfate salt monohydrate, 0.05% w/v Tryptamine, 0.05% w/v Arbutin (in 50% EtOH)
Protein and Ligand in 50mM Tris, 150mM NaCl, 2mM TCEP, 0.04% NaN3, pH: 7.5 Buffer
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.526 α = 90 b = 101.805 β = 111.128 c = 114.133 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 X 16M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033220 PETRA III, DESY P11
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 2.94 48.72 98.5 0.094 0.13 0.09 0.996 8 3.5 43555
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 2.94 3.06 0.672 0.923 0.629 0.509 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.945 48.715 43523 2105 98.273 0.25 0.2464 0.2464 0.3166 0.3166 83.416
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] -0.559 1.168 -1.677 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.25 r_dihedral_angle_3_deg 15.385 r_lrange_other 14.689 r_lrange_it 14.688 r_mcangle_it 7.991 r_mcangle_other 7.991 r_scangle_it 7.825 r_scangle_other 7.825 r_dihedral_angle_2_deg 7.16 r_dihedral_angle_1_deg 7.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.25 r_dihedral_angle_3_deg 15.385 r_lrange_other 14.689 r_lrange_it 14.688 r_mcangle_it 7.991 r_mcangle_other 7.991 r_scangle_it 7.825 r_scangle_other 7.825 r_dihedral_angle_2_deg 7.16 r_dihedral_angle_1_deg 7.051 r_mcbond_it 4.908 r_mcbond_other 4.908 r_scbond_it 4.629 r_scbond_other 4.627 r_angle_refined_deg 1.577 r_symmetry_xyhbond_nbd_refined 0.605 r_angle_other_deg 0.506 r_symmetry_nbd_refined 0.496 r_nbd_other 0.469 r_nbd_refined 0.208 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.074 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.058 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14632 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing