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Crystal structure of the motor domain of human kinesin family member 3B 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 8.5 291 30% PEG 3350, 0.1 M Tris-HCl, 0.2M Lithium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.731 α = 90 b = 95.852 β = 92.61 c = 63.883 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 IMAGE PLATE RIGAKU RAXIS IV++ 2007-08-08 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 1.8 20 98.9 0.05 17.1 3.6 64524
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) 1.8 1.86 96.7 0.377 3.4 6271
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 (All) 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 1GOJ 1.8 19.86 64496 2083 98.83 0.192 0.192 0.191 0.1935 0.233 0.2346 thin shells 19.167
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] -0.15 -0.35 0.99 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 15.464 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.98 r_scangle_it 3.972 r_mcangle_it 3.243 r_scbond_it 2.879 r_mcbond_it 2.442 r_angle_refined_deg 1.458 r_angle_other_deg 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.616 r_dihedral_angle_4_deg 15.464 r_dihedral_angle_3_deg 13.154 r_dihedral_angle_1_deg 5.98 r_scangle_it 3.972 r_mcangle_it 3.243 r_scbond_it 2.879 r_mcbond_it 2.442 r_angle_refined_deg 1.458 r_angle_other_deg 0.958 r_mcbond_other 0.76 r_symmetry_vdw_other 0.251 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.203 r_nbd_other 0.196 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_metal_ion_refined 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5110 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 61
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction