3V3L | pdb_00003v3l

Crystal structure of human RNF146 WWE domain in complex with iso-ADPRibose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829545% PEG 400, 100 mM Tris HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.1661.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.343α = 90
b = 55.343β = 90
c = 146.471γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.632032399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.6896

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.652029606157599.50.1530.1510.16370.1810.1896RANDOM32.28
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]
-0.95-0.47-0.951.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.121
r_dihedral_angle_4_deg16.471
r_dihedral_angle_3_deg15.766
r_scangle_it8.227
r_dihedral_angle_1_deg6.784
r_scbond_it5.782
r_mcangle_it5.28
r_mcbond_it3.406
r_rigid_bond_restr1.795
r_angle_refined_deg1.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.121
r_dihedral_angle_4_deg16.471
r_dihedral_angle_3_deg15.766
r_scangle_it8.227
r_dihedral_angle_1_deg6.784
r_scbond_it5.782
r_mcangle_it5.28
r_mcbond_it3.406
r_rigid_bond_restr1.795
r_angle_refined_deg1.573
r_mcbond_other1.39
r_angle_other_deg0.815
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1422
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms72

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling