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Crystal structure of human katanin AAA ATPase domain complex with ATPgammaS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.4 M Calcium acetate
20% (v/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.907 α = 90 b = 68.907 β = 90 c = 138.698 γ = 120
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 ADSC QUANTUM 315r 2016-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9794 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.9 50 98.5 0.109 0.115 0.036 11 7.8 8212 61.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 91.5 0.386 0.454 0.231 0.083 3.1
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 5ZQL 2.9 45.234 7788 393 98.45 0.24927 0.24735 0.2481 0.28514 0.283 RANDOM 74.619
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] 0.44 0.22 0.44 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.312 r_dihedral_angle_3_deg 19.811 r_long_range_B_refined 14.66 r_long_range_B_other 14.658 r_dihedral_angle_4_deg 11.807 r_mcangle_it 8.75 r_mcangle_other 8.748 r_scangle_other 8.666 r_dihedral_angle_1_deg 7.493 r_mcbond_other 5.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.312 r_dihedral_angle_3_deg 19.811 r_long_range_B_refined 14.66 r_long_range_B_other 14.658 r_dihedral_angle_4_deg 11.807 r_mcangle_it 8.75 r_mcangle_other 8.748 r_scangle_other 8.666 r_dihedral_angle_1_deg 7.493 r_mcbond_other 5.319 r_mcbond_it 5.317 r_scbond_it 5.146 r_scbond_other 5.144 r_angle_refined_deg 1.633 r_angle_other_deg 1.01 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2304 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing