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Crystal Structure of the KIF5C Motor Domain Without Any Nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 Ammonium sulfate, Sodium citrate, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.94 58.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.585 α = 90 b = 71.322 β = 90 c = 176.163 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 95 CCD ADSC QUANTUM 210 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
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 2.86 50 99.7 0.079 14.4 7.2 21497 21432
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 2.86 2.91 100 0.942 6.9 1015
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2KIN 2.86 20 21469 21376 1096 99.57 0.2405 0.2373 0.2362 0.2993 0.2992 RANDOM 102.294
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] -2.16 0.94 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.695 r_dihedral_angle_3_deg 20.688 r_dihedral_angle_4_deg 19.691 r_mcangle_it 12.028 r_scbond_it 9.166 r_mcbond_it 8.065 r_dihedral_angle_1_deg 5.923 r_angle_refined_deg 1.648 r_chiral_restr 0.104 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.695 r_dihedral_angle_3_deg 20.688 r_dihedral_angle_4_deg 19.691 r_mcangle_it 12.028 r_scbond_it 9.166 r_mcbond_it 8.065 r_dihedral_angle_1_deg 5.923 r_angle_refined_deg 1.648 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4980 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling