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Motor domain of Neurospora crassa kinesin-3 (NcKin3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I5S TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 1.5ul protein solution (50mM phosphate buffer pH 7.5, 150mM sodium chloride, 50uM ATP, 1mM magnesium chloride, EGTA, DTT) mixed with 0.5ul reservoir (0.1M Hepes pH 7.5, 0.2M sodium potassium tartrate, 24% PEG3350) and 0.2ul 0.1M magnesium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.945 α = 90 b = 98.408 β = 91.86 c = 111.764 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2004-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 3.25 111.8 100 0.143 6 3.8 26100
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 3.25 3.31 100 0.705 3.8
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 TRUNCATED MODEL DERIVED FROM ADP COMPLEX OF KIF1A (1I5S) 3.25 111.8 26084 24755 1329 100 0.213 0.21 0.2092 0.256 0.2522 RANDOM 74.79
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] 1.87 5.06 0.85 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_3_deg 22.912 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_1_deg 7.38 r_scangle_it 1.867 r_angle_refined_deg 1.844 r_scbond_it 1.122 r_mcangle_it 0.669 r_symmetry_hbond_refined 0.425 r_mcbond_it 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_3_deg 22.912 r_dihedral_angle_4_deg 19.541 r_dihedral_angle_1_deg 7.38 r_scangle_it 1.867 r_angle_refined_deg 1.844 r_scbond_it 1.122 r_mcangle_it 0.669 r_symmetry_hbond_refined 0.425 r_mcbond_it 0.386 r_nbtor_refined 0.338 r_symmetry_vdw_refined 0.295 r_nbd_refined 0.261 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.118 r_metal_ion_refined 0.073 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10226 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction