3NG2

Crystal structure of the RNF4 ring domain dimer


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22910.2M lithium sulfate, 0.1M bis-Tris, 22% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.77841330.837214

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.487α = 90
b = 85.922β = 90
c = 22.277γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDADSC QUANTUM 210r2009-07-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.2829, 1.2833, 1.2523Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.819.0199.10.0670.06716.16.6110411093618.3
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)
1.81.998.80.2746.76.61571

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 DIFFRACTIONMADTHROUGHOUT1.818.731034954898.70.190010.187290.24199RANDOM24.027
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]
0.480.91-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.216
r_dihedral_angle_4_deg17.562
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg10.746
r_scangle_it3.715
r_scbond_it2.27
r_mcangle_it1.723
r_angle_refined_deg1.546
r_mcbond_it0.974
r_chiral_restr0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.216
r_dihedral_angle_4_deg17.562
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg10.746
r_scangle_it3.715
r_scbond_it2.27
r_mcangle_it1.723
r_angle_refined_deg1.546
r_mcbond_it0.974
r_chiral_restr0.134
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1038
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms9

Software

Software
Software NamePurpose
SHARPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling