8KG2

Crystal structure of p97-N/D1 hexamer in complex with FAF1-UBX domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DYG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62950.2M sodium acetate, 0.1M sodium citrate (pH 5.6), 5% polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
2.8757.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.665α = 71.52
b = 134.484β = 80.87
c = 148.223γ = 87.53
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0000Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
13.148.897.40.0880.9987.73.9150419
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.150.8390.7041.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.148.8129500679897.360.200160.197690.24626RANDOM91.028
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]
3.912.831.86-0.141.64-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined25.199
r_dihedral_angle_3_deg21.19
r_dihedral_angle_2_deg15.505
r_mcangle_it14.991
r_scbond_it12.089
r_mcbond_it9.646
r_dihedral_angle_1_deg5.993
r_angle_refined_deg1.56
r_chiral_restr0.109
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined25.199
r_dihedral_angle_3_deg21.19
r_dihedral_angle_2_deg15.505
r_mcangle_it14.991
r_scbond_it12.089
r_mcbond_it9.646
r_dihedral_angle_1_deg5.993
r_angle_refined_deg1.56
r_chiral_restr0.109
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48411
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms324

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing