5M37

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 DROP277.150.17 M Ammonium acetate;0.085 M tri-Sodium citrate pH 5.6; 25.5 %(w/v) PEG 4000; 15 %(v/v) Glycerol
Crystal Properties
Matthews coefficientSolvent content
3.160.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.17α = 90
b = 88.21β = 90
c = 112.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.998SLSX10SA

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
12.3549.799.60.0790.0830.99920.5613.00130145-357.578
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)
12.352.699.60.8070.8410.973.6112.768

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 REPLACEMENTTHROUGHOUT3NKX2.3549.728587150599.640.2250.22230.2751RANDOM62.534
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]
-6.1910.17-3.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.004
r_dihedral_angle_4_deg15.69
r_dihedral_angle_3_deg15.303
r_dihedral_angle_1_deg4.916
r_angle_refined_deg1.399
r_angle_other_deg1.229
r_chiral_restr0.073
r_gen_planes_other0.014
r_bond_refined_d0.011
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.004
r_dihedral_angle_4_deg15.69
r_dihedral_angle_3_deg15.303
r_dihedral_angle_1_deg4.916
r_angle_refined_deg1.399
r_angle_other_deg1.229
r_chiral_restr0.073
r_gen_planes_other0.014
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3820
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms226

Software

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