3HU2

Structure of p97 N-D1 R86A mutant in complex with ATPgS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8288100mM NaCl, 4% benzamidine, 100mM citrate, pH 5.8, 16.5% PEG3350 and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
3.0359.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.892α = 97.52
b = 102.645β = 90.63
c = 107.182γ = 91.45
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
12.85400.04913.885163

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 REPLACEMENTTHROUGHOUT2.854079168419493.010.259360.257730.29027RANDOM70.682
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]
3.47-0.140.9-0.62-2.48-3.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.298
r_dihedral_angle_3_deg19.527
r_dihedral_angle_4_deg16.891
r_dihedral_angle_1_deg6.074
r_scangle_it1.646
r_angle_refined_deg1.52
r_scbond_it1.124
r_mcangle_it0.65
r_mcbond_it0.433
r_symmetry_hbond_refined0.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.298
r_dihedral_angle_3_deg19.527
r_dihedral_angle_4_deg16.891
r_dihedral_angle_1_deg6.074
r_scangle_it1.646
r_angle_refined_deg1.52
r_scbond_it1.124
r_mcangle_it0.65
r_mcbond_it0.433
r_symmetry_hbond_refined0.325
r_nbtor_refined0.264
r_symmetry_vdw_refined0.222
r_metal_ion_refined0.211
r_nbd_refined0.161
r_chiral_restr0.127
r_xyhbond_nbd_refined0.107
r_bond_refined_d0.02
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21168
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms192

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling