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Structure of spastin AAA domain (T692A mutant) in complex with JNJ-7706621 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9P PDB entry 3B9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M sodium acetate, pH 5.0-7.0, 2% PEG4000, 15% MPD
Crystal Properties Matthews coefficient Solvent content 2.58 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.446 α = 90 b = 79.446 β = 90 c = 97.171 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 PIXEL DECTRIS EIGER X 9M 2018-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 2.15 50 99.8 0.035 10.6 5.5 18983 -3 46.9707656484
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 2.15 2.19 99.9 0.391 2.667 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3B9P 2.15 39.6875727494 1.38897488545 18944 1889 99.8103266596 0.215347370249 0.212595700008 0.2128 0.240981213524 0.2416 55.8610370905
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.7148324684 f_angle_d 0.413208023194 f_chiral_restr 0.0372083766985 f_plane_restr 0.00231430244276 f_bond_d 0.00166467485052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2027 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing