3TC5

Selective targeting of disease-relevant protein binding domains by O-phosphorylated natural product derivatives


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400,pH 7.5, vapor diffusion, sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.957.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.36α = 90
b = 68.36β = 90
c = 79.37γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77PIXELPSI PILATUS 6M2010-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.45998.34274842028-3
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)
11.41.796.90.3384.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2ZR61.419.734202832347173579.820.176630.174830.21098RANDOM15.45
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.728
r_dihedral_angle_4_deg19.902
r_dihedral_angle_3_deg12.303
r_dihedral_angle_1_deg5.907
r_scangle_it2.679
r_scbond_it1.743
r_angle_refined_deg1.146
r_mcangle_it1.108
r_angle_other_deg0.758
r_rigid_bond_restr0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.728
r_dihedral_angle_4_deg19.902
r_dihedral_angle_3_deg12.303
r_dihedral_angle_1_deg5.907
r_scangle_it2.679
r_scbond_it1.743
r_angle_refined_deg1.146
r_mcangle_it1.108
r_angle_other_deg0.758
r_rigid_bond_restr0.7
r_mcbond_it0.648
r_mcbond_other0.205
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1135
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms51

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling