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Crystal structure of the human KIF9 motor domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOJ pdb entry 1GOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 1.5M ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.443 α = 90 b = 90.443 β = 90 c = 76.38 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE 2006-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 30 99.1 0.059 18.2 5.2 46976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 99.5 0.411 5.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1GOJ 2 29.173 22881 1145 95.072 0.226 0.2238 0.277 0.264 random 28.19
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] -0.349 -0.175 -0.349 0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.365 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_1_deg 6.069 r_mcangle_it 3.679 r_scangle_it 3.514 r_mcbond_it 2.81 r_scbond_it 2.659 r_angle_refined_deg 1.414 r_angle_other_deg 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.365 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_1_deg 6.069 r_mcangle_it 3.679 r_scangle_it 3.514 r_mcbond_it 2.81 r_scbond_it 2.659 r_angle_refined_deg 1.414 r_angle_other_deg 1.4 r_mcbond_other 0.59 r_symmetry_vdw_other 0.208 r_symmetry_vdw_refined 0.206 r_nbd_other 0.2 r_nbd_refined 0.186 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.081 r_nbtor_other 0.079 r_metal_ion_refined 0.058 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction