5M36

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
3.766.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.52α = 90
b = 102.36β = 90
c = 112.82γ = 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 X10SA0.989SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.4546.6199.90.0570.06126.6813.06631166-368.78
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.699.80.9230.9610.9593.113.014

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 REPLACEMENTTHROUGHOUT3NKX2.4546.6129554155599.90.22640.22380.2736RANDOM77.665
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]
-6.48.89-2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.922
r_dihedral_angle_4_deg17.045
r_dihedral_angle_3_deg15.346
r_dihedral_angle_1_deg5.711
r_angle_refined_deg1.376
r_angle_other_deg1.214
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.922
r_dihedral_angle_4_deg17.045
r_dihedral_angle_3_deg15.346
r_dihedral_angle_1_deg5.711
r_angle_refined_deg1.376
r_angle_other_deg1.214
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3679
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms244

Software

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