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Crystal structure of the human KIF2 motor domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V8K PDB entry 1V8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.475 α = 90 b = 121.475 β = 90 c = 175.684 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 100 IMAGE PLATE RIGAKU RAXIS 2006-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 2.35 30 100 0.068 12.1 8.1 21011
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) 1 2.35 2.43 100 0.95 7.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1V8K 2.35 29.285 20965 1077 99.795 0.224 0.2215 0.2991 0.2833 0.334 random 57.036
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] 0.297 0.149 0.297 -0.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_1_deg 6.419 r_scangle_it 3.862 r_mcangle_it 3.518 r_scbond_it 2.814 r_mcbond_it 2.467 r_angle_refined_deg 1.394 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.455 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 14.673 r_dihedral_angle_1_deg 6.419 r_scangle_it 3.862 r_mcangle_it 3.518 r_scbond_it 2.814 r_mcbond_it 2.467 r_angle_refined_deg 1.394 r_nbtor_refined 0.302 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction