5M35

The molecular tweezer CLR01 stabilizes a disordered protein-protein interface


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6277.150.17 M Ammonium acetate; 0.085 M Sodium citrate pH 5.6; 25.5%(w/v) PEG 4000; 15%(v/v) Glycerol
Crystal Properties
Matthews coefficientSolvent content
3.9468.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.221α = 90
b = 104.075β = 90
c = 114.451γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99983SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.3844.8599.70.0660.99916.766.435499-358.906
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.382.599.90.5980.7573.11

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 REPLACEMENTTHROUGHOUT3NKX2.3844.853312317461000.22710.22430.2772RANDOM55.997
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]
-0.443.6-3.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.41
r_dihedral_angle_3_deg21.123
r_dihedral_angle_4_deg15.705
r_dihedral_angle_1_deg15.346
r_scangle_it5.159
r_scbond_it3.189
r_mcangle_it2.14
r_angle_refined_deg1.9
r_mcbond_it1.111
r_angle_other_deg1.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.41
r_dihedral_angle_3_deg21.123
r_dihedral_angle_4_deg15.705
r_dihedral_angle_1_deg15.346
r_scangle_it5.159
r_scbond_it3.189
r_mcangle_it2.14
r_angle_refined_deg1.9
r_mcbond_it1.111
r_angle_other_deg1.034
r_chiral_restr0.133
r_bond_refined_d0.021
r_bond_other_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3655
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms30

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata reduction
PHASERphasing