3HU1

Structure of p97 N-D1 R95G 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
3.1360.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.756α = 97.66
b = 103.279β = 91.88
c = 107.688γ = 89.75
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
12.8143.920.0512.315140687240

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 REPLACEMENTTHROUGHOUT2.812582809432390.150.241410.239880.27144RANDOM64.976
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]
1.720.741.17-0.23-1.27-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.368
r_dihedral_angle_3_deg20.019
r_dihedral_angle_4_deg17.786
r_dihedral_angle_1_deg6.027
r_scangle_it1.785
r_angle_refined_deg1.507
r_scbond_it1.216
r_mcangle_it0.698
r_mcbond_it0.472
r_symmetry_hbond_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.368
r_dihedral_angle_3_deg20.019
r_dihedral_angle_4_deg17.786
r_dihedral_angle_1_deg6.027
r_scangle_it1.785
r_angle_refined_deg1.507
r_scbond_it1.216
r_mcangle_it0.698
r_mcbond_it0.472
r_symmetry_hbond_refined0.306
r_nbtor_refined0.263
r_symmetry_vdw_refined0.228
r_metal_ion_refined0.187
r_nbd_refined0.161
r_chiral_restr0.129
r_xyhbond_nbd_refined0.108
r_bond_refined_d0.021
r_gen_planes_refined0.014
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 Atoms21132
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms192

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling