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Crystal structure of KIF1A Motor-Neck domain with ADP-Mg-AlFx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, Ammonium acetate, Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.09 41.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.502 α = 90 b = 57.319 β = 90 c = 154.826 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 PIXEL DECTRIS EIGER X 16M 2018-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.57 30 96.8 0.081 0.063 0.997 10.1 6.1 11987 39.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.63 100 0.517 0.307 0.898 1.8 6.5
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 (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 1VFX 2.57 28.68 11371 616 96.7 0.2259 0.2252 0.2276 0.2389 0.2373 RANDOM 48.26
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] -3.03 8.39 -5.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_3_deg 17.591 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_1_deg 7.65 r_angle_refined_deg 1.529 r_angle_other_deg 1.3 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_3_deg 17.591 r_dihedral_angle_4_deg 17.585 r_dihedral_angle_1_deg 7.65 r_angle_refined_deg 1.529 r_angle_other_deg 1.3 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 2745 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing