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Crystal structure of the TPR domain of KLC1 in complex with an engineered high-affinity cargo peptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NF1 3NF1, 6FV0 experimental model PDB 6FV0 3NF1, 6FV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 300 0.1 M MIB buffer pH 9.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.68 54.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.732 α = 90 b = 107.532 β = 90 c = 222.65 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 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.849 111.325 99.3 0.114 0.131 0.063 0.994 8 4.47 57529
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 2.85 2.9 97.1 1.543 1.791 0.889 0.365 1.2 4.42
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NF1, 6FV0 2.849 111.325 57431 2703 99.18 0.203 0.2015 0.2017 0.2426 0.2424
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] -3.114 -2.107 5.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 16.874 r_lrange_it 8.228 r_lrange_other 8.228 r_dihedral_angle_1_deg 4.841 r_scangle_it 4.36 r_scangle_other 4.36 r_mcangle_it 3.664 r_mcangle_other 3.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.418 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 16.874 r_lrange_it 8.228 r_lrange_other 8.228 r_dihedral_angle_1_deg 4.841 r_scangle_it 4.36 r_scangle_other 4.36 r_mcangle_it 3.664 r_mcangle_other 3.664 r_scbond_it 2.654 r_scbond_other 2.654 r_mcbond_it 2.244 r_mcbond_other 2.243 r_angle_refined_deg 1.421 r_angle_other_deg 1.269 r_symmetry_xyhbond_nbd_refined 0.307 r_nbd_other 0.213 r_symmetry_nbd_refined 0.211 r_nbd_refined 0.206 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_4 0.117 r_ncsr_local_group_8 0.116 r_ncsr_local_group_1 0.115 r_ncsr_local_group_13 0.114 r_ncsr_local_group_3 0.113 r_ncsr_local_group_11 0.112 r_ncsr_local_group_15 0.111 r_ncsr_local_group_10 0.108 r_ncsr_local_group_2 0.107 r_ncsr_local_group_6 0.107 r_ncsr_local_group_9 0.107 r_ncsr_local_group_7 0.105 r_ncsr_local_group_5 0.103 r_ncsr_local_group_12 0.102 r_ncsr_local_group_14 0.102 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13783 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling REFMAC phasing