2HPL

Crystal structure of the mouse p97/PNGase complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1828118-22% PEG 5000 MME and 14-18% Tacsimate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.608α = 90
b = 52.42β = 115.33
c = 35.028γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.04NSLSX26C

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
11.85087.70.0614.45.88764
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8646.10.3143.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONREFMAC 5.2.0005THROUGHOUT1.8203033875342887.80.1460.185RANDOM18.76
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]
2.840.01-0.9-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.053
r_dihedral_angle_4_deg16.512
r_dihedral_angle_3_deg14.384
r_dihedral_angle_1_deg5.664
r_scangle_it3.494
r_scbond_it2.515
r_angle_refined_deg1.479
r_mcangle_it1.396
r_mcbond_it1.232
r_angle_other_deg0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.053
r_dihedral_angle_4_deg16.512
r_dihedral_angle_3_deg14.384
r_dihedral_angle_1_deg5.664
r_scangle_it3.494
r_scbond_it2.515
r_angle_refined_deg1.479
r_mcangle_it1.396
r_mcbond_it1.232
r_angle_other_deg0.87
r_symmetry_vdw_other0.313
r_mcbond_other0.258
r_nbd_refined0.229
r_nbd_other0.2
r_symmetry_vdw_refined0.185
r_nbtor_refined0.182
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.159
r_nbtor_other0.089
r_chiral_restr0.085
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms827
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing