8HRZ

Crystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S3S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729514% PEG 3350, 0.2M ammonium citrate tribasic (pH 7), 0.01M hexamine cobalt (III) chloride
Crystal Properties
Matthews coefficientSolvent content
3.2562.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.78α = 90
b = 178.85β = 119.8
c = 171.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
12.740.01399.30.0380.9999.47.4242685
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.750.540.53

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.740.0132426561193899.3010.2150.21320.255871.106
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]
-0.8210.1144.489-2.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.467
r_lrange_it19.433
r_dihedral_angle_6_deg15.777
r_scangle_it14.595
r_dihedral_angle_1_deg13.67
r_mcangle_it12.298
r_scbond_it10.028
r_mcbond_it8.25
r_dihedral_angle_2_deg5.722
r_angle_refined_deg1.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.467
r_lrange_it19.433
r_dihedral_angle_6_deg15.777
r_scangle_it14.595
r_dihedral_angle_1_deg13.67
r_mcangle_it12.298
r_scbond_it10.028
r_mcbond_it8.25
r_dihedral_angle_2_deg5.722
r_angle_refined_deg1.663
r_nbtor_refined0.314
r_symmetry_xyhbond_nbd_refined0.258
r_nbd_refined0.252
r_symmetry_nbd_refined0.168
r_xyhbond_nbd_refined0.156
r_chiral_restr0.126
r_bond_refined_d0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48760
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms324

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing