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Crystal Structure Analysis of Human Kinesin-8 Motor Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5C PDB ENTRY 1T5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 275 10-13% PEG 20000, 0.1M HEPES pH 7.8, 2% dioxane, vapor diffusion, temperature 275K
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.42 α = 90 b = 79.744 β = 90 c = 140.145 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 CCD BRUKER AXS PROTEUM/R6000 MIRRORS 2004-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 70.71 98.8 0.064 6.9 39803
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 PDB ENTRY 1T5C 2.2 70.71 39755 1988 98.62 0.223 0.221 0.2227 0.277 0.2765 RANDOM 33.274
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] -0.14 0.71 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.498 r_scangle_it 4.102 r_scbond_it 2.454 r_mcangle_it 1.873 r_angle_refined_deg 1.699 r_mcbond_it 1.005 r_angle_other_deg 0.925 r_symmetry_vdw_other 0.269 r_nbd_other 0.243 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.498 r_scangle_it 4.102 r_scbond_it 2.454 r_mcangle_it 1.873 r_angle_refined_deg 1.699 r_mcbond_it 1.005 r_angle_other_deg 0.925 r_symmetry_vdw_other 0.269 r_nbd_other 0.243 r_nbd_refined 0.221 r_chiral_restr 0.199 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.194 r_symmetry_vdw_refined 0.155 r_nbtor_other 0.087 r_metal_ion_refined 0.065 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 56
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection PROTEUM PLUS data reduction LSCALE data scaling MOLREP phasing