6P13

Structure of spastin AAA domain (T692A mutant) in complex with a diaminotriazole-based inhibitor (crystal form A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B9PPDB entry 3B9P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M sodium acetate, pH 5.0-6.5, 2% PEG4000, 15% MPD
Crystal Properties
Matthews coefficientSolvent content
2.5852.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.698α = 90
b = 79.698β = 90
c = 96.873γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9201NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15099.90.04313.45.82042346.0316109984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141000.4480.8692.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3B9P2.139.8491.3820389204899.880.21060.20670.245450.7305
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.113
f_angle_d0.487
f_chiral_restr0.039
f_bond_d0.003
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2040
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms41

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing