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The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with ADP-Mg-AlFx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 potassium sodium tartrate tetrahydrate, MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.098 α = 90 b = 166.989 β = 90 c = 74.991 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 2M-F 2017-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.98 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.43 30 99.9 0.163 0.068 11.9 6.1 15927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.43 3.52 100 0.647 0.273 2.2 6.4
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 1V8J 3.43 30 15064 846 99.76 0.1994 0.1976 0.2011 0.2303 0.2372 RANDOM 67.344
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] 5.86 -3.29 -2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 18.832 r_dihedral_angle_3_deg 16.67 r_dihedral_angle_1_deg 6.829 r_angle_refined_deg 1.818 r_angle_other_deg 1.388 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.958 r_dihedral_angle_4_deg 18.832 r_dihedral_angle_3_deg 16.67 r_dihedral_angle_1_deg 6.829 r_angle_refined_deg 1.818 r_angle_other_deg 1.388 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5268 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing