3D2W

Crystal structure of mouse TDP-43 RRM2 domain in complex with DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2298Reservoir solution containing 2M (NH4)2SO4, 0.1M phosphate-citrate, the reservoir solution contained an addition of 10% glycerol, pH4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.283α = 90
b = 87.29β = 90
c = 125.345γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123CCDADSC QUANTUM 2102008-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C11NSRRCBL13C1

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
11.6525.4698.70.0580.058144.713674138541.8728.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.71970.320.323.514.51310

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 ENTRY 1WF01.6525.461263312633104198.740.210310.207280.24515RANDOM23.14
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]
-0.04-0.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.762
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg14.735
r_dihedral_angle_1_deg4.855
r_scangle_it2.567
r_scbond_it1.676
r_mcangle_it1.484
r_angle_refined_deg1.257
r_mcbond_it0.839
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.762
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg14.735
r_dihedral_angle_1_deg4.855
r_scangle_it2.567
r_scbond_it1.676
r_mcangle_it1.484
r_angle_refined_deg1.257
r_mcbond_it0.839
r_nbtor_refined0.309
r_nbd_refined0.187
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.132
r_chiral_restr0.076
r_bond_refined_d0.009
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 Atoms561
Nucleic Acid Atoms186
Solvent Atoms116
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing