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Kinesin-like protein at 61F (Klp61f) bound to AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 10% ethylene glycol, 50mM 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid sodium salt (sodium HEPES) pH 7.5, 180mM NaI and 15-17% polyethylene glycol MW 3,350
Crystal Properties Matthews coefficient Solvent content 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.692 α = 78.532 b = 50.813 β = 77.869 c = 93.344 γ = 73.197
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 Platinum 135 Helios 2012-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 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 1.74 48.11 91.8 0.0569 12.56 3.31 67986
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 1.74 1.84 0.2722 2.5
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3HQD 1.744 48.11 67044 2669 90.616 0.187 0.185 0.2238 0.2357 29.723
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] -0.593 0.341 0.235 0.678 -0.956 -0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.05 r_dihedral_angle_3_deg 18.326 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_1_deg 7.698 r_lrange_it 6.508 r_lrange_other 6.507 r_scangle_it 3.755 r_scangle_other 3.754 r_mcangle_it 3.082 r_mcangle_other 3.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.05 r_dihedral_angle_3_deg 18.326 r_dihedral_angle_4_deg 16.63 r_dihedral_angle_1_deg 7.698 r_lrange_it 6.508 r_lrange_other 6.507 r_scangle_it 3.755 r_scangle_other 3.754 r_mcangle_it 3.082 r_mcangle_other 3.081 r_scbond_it 2.311 r_scbond_other 2.31 r_angle_refined_deg 1.953 r_mcbond_it 1.833 r_mcbond_other 1.833 r_angle_other_deg 1.457 r_xyhbond_nbd_other 0.371 r_symmetry_xyhbond_nbd_refined 0.328 r_symmetry_nbd_refined 0.271 r_nbd_other 0.257 r_nbd_refined 0.234 r_symmetry_nbd_other 0.207 r_xyhbond_nbd_refined 0.204 r_symmetry_xyhbond_nbd_other 0.179 r_nbtor_refined 0.164 r_chiral_restr 0.096 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.089 r_chiral_restr_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5431 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SAINT data scaling AMoRE phasing