4M7C

Crystal structure of the TRF2-binding motif of SLX4 in complex with the TRFH domain of TRF2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BU8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.427710% PEG 4000, 0.1M HEPES, pH 7.4, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.591α = 90
b = 69.183β = 94.73
c = 118.078γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F1.0000APS21-ID-F

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
12.0510096.70.0689.23.932186
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)
12.052.1295.60.2873.73114

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 REPLACEMENTTHROUGHOUT3BU82.0544.8631784160996.340.21650.21410.262RANDOM24.9856
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]
-1.061.52-0.271.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.833
r_sphericity_free30.179
r_sphericity_bonded23.223
r_dihedral_angle_4_deg15.44
r_dihedral_angle_3_deg14.969
r_dihedral_angle_1_deg4.337
r_rigid_bond_restr4.301
r_angle_refined_deg0.866
r_chiral_restr0.063
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.833
r_sphericity_free30.179
r_sphericity_bonded23.223
r_dihedral_angle_4_deg15.44
r_dihedral_angle_3_deg14.969
r_dihedral_angle_1_deg4.337
r_rigid_bond_restr4.301
r_angle_refined_deg0.866
r_chiral_restr0.063
r_bond_refined_d0.004
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3394
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing