6RKM

Fragment AZ-022 binding at the p53pT387/14-3-3 sigma interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MOC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.1M Hepes, pH7.5, 27%PEG, 5% Glycerol, 0.2M Calcium Chloride, 2mM DTT.
Crystal Properties
Matthews coefficientSolvent content
2.6453.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.78α = 90
b = 112.51β = 90
c = 62.59γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2017-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBERIGAKU MICROMAX-0031.54187

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8826.49870.1250.9758.548107920426
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9386.40.40.8653.13.84927

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 REPLACEMENTFREE R-VALUE5MOC1.8826.49193371075860.180770.178080.22994RANDOM12.74
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]
0.27-0.03-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.879
r_dihedral_angle_3_deg13.992
r_dihedral_angle_4_deg12.806
r_dihedral_angle_1_deg5.708
r_long_range_B_refined5.459
r_long_range_B_other4.868
r_scangle_other2.649
r_mcangle_it1.779
r_mcangle_other1.779
r_scbond_it1.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.879
r_dihedral_angle_3_deg13.992
r_dihedral_angle_4_deg12.806
r_dihedral_angle_1_deg5.708
r_long_range_B_refined5.459
r_long_range_B_other4.868
r_scangle_other2.649
r_mcangle_it1.779
r_mcangle_other1.779
r_scbond_it1.711
r_scbond_other1.71
r_angle_refined_deg1.466
r_mcbond_it1.101
r_mcbond_other1.101
r_angle_other_deg1.037
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1881
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing