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Human KIF18A-DARPin fusion protein bound to AMP-PNP and tubulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DRX in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M ammonium nitrate, 0.1 M sodium acetate pH 5.6, 20% (w/v) PEG Smear Low (5% PEG 400, 5% PEG 500 MME, 5% PEG 600, 5% PEG 1000), 5% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.38 α = 90 b = 135.47 β = 107.673 c = 117.67 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 EIGER X 16M 2024-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 SPring-8 BL45XU
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 2.406 48.673 99.4 0.091 0.999 12.3 7.1 121098
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 2.41 2.45 0.885
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 THROUGHOUT 2.406 48.673 121097 6162 99.265 0.193 0.1907 0.1926 0.2377 0.2379 61.972
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] 1.022 0.257 2.827 -3.336
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.175 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_6_deg 12.591 r_scangle_it 11.61 r_mcangle_it 11.156 r_scbond_it 7.212 r_mcbond_it 6.739 r_dihedral_angle_1_deg 5.99 r_dihedral_angle_2_deg 3.405 r_rigid_bond_restr 1.946
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.175 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_6_deg 12.591 r_scangle_it 11.61 r_mcangle_it 11.156 r_scbond_it 7.212 r_mcbond_it 6.739 r_dihedral_angle_1_deg 5.99 r_dihedral_angle_2_deg 3.405 r_rigid_bond_restr 1.946 r_angle_refined_deg 1.061 r_nbtor_refined 0.298 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.13 r_ncsr_local_group_3 0.116 r_symmetry_xyhbond_nbd_refined 0.109 r_ncsr_local_group_2 0.092 r_chiral_restr 0.083 r_ncsr_local_group_1 0.081 r_ncsr_local_group_4 0.08 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20956 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing