2ZNV

Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293180mM tri-ammonium citrate (pH 7.0), 24% PEG 3350, 3% 1,6-Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.089α = 90
b = 97.363β = 97.49
c = 87.894γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2008-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

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
11.687.0497.30.06816.98368383683-0.5
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)
1.61.6290.70.2673.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 ENTRIES 2ZNR and 1ubq1.632.478368377359405197.150.185110.18350.21522RANDOM15.093
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]
-0.250.150.020.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg17.307
r_dihedral_angle_3_deg12.863
r_dihedral_angle_1_deg5.747
r_scangle_it3.724
r_scbond_it2.248
r_mcangle_it1.48
r_angle_refined_deg1.265
r_mcbond_it0.858
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.822
r_dihedral_angle_4_deg17.307
r_dihedral_angle_3_deg12.863
r_dihedral_angle_1_deg5.747
r_scangle_it3.724
r_scbond_it2.248
r_mcangle_it1.48
r_angle_refined_deg1.265
r_mcbond_it0.858
r_nbtor_refined0.306
r_symmetry_vdw_refined0.218
r_nbd_refined0.2
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.14
r_chiral_restr0.087
r_bond_refined_d0.01
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 Atoms5072
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing