2ZJD

Crystal Structure of LC3-p62 complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52880.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.1542.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.559α = 90
b = 39.592β = 93.3
c = 78.011γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402007-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.5577.8598.40.05423.94.539943
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)
1.551.61860.314.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1UGM1.5645.4837918200599.270.202810.2010.23766RANDOM19.107
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]
0.30.71-0.850.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.241
r_dihedral_angle_4_deg15.429
r_dihedral_angle_3_deg11.574
r_dihedral_angle_1_deg6.218
r_scangle_it3.557
r_scbond_it2.283
r_mcangle_it1.674
r_angle_refined_deg1.298
r_mcbond_it1.037
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.241
r_dihedral_angle_4_deg15.429
r_dihedral_angle_3_deg11.574
r_dihedral_angle_1_deg6.218
r_scangle_it3.557
r_scbond_it2.283
r_mcangle_it1.674
r_angle_refined_deg1.298
r_mcbond_it1.037
r_nbtor_refined0.304
r_nbd_refined0.209
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.132
r_xyhbond_nbd_refined0.125
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.005
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_refined
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 Atoms2152
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing