2XP5

DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRUCTURE-GUIDED FRAGMENT EVOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KCEPDB ENTRY 3KCE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52772.2M AMMONIUM SULPHATE, 0.1M HEPES BUFFER, 1% PEG 400, 5MM DTT, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.8757

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.398α = 90
b = 68.398β = 90
c = 79.488γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATERIGAKU IMAGE PLATEMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.93096.50.069.72.76168262
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)
11.991.80.372.32.35

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3KCE1.959.231596486096.370.200410.198670.23238RANDOM33.052
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]
0.870.440.87-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg23.966
r_dihedral_angle_3_deg17.925
r_dihedral_angle_1_deg7.623
r_scangle_it6.308
r_scbond_it4.016
r_mcangle_it2.437
r_angle_refined_deg2.177
r_mcbond_it1.347
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg23.966
r_dihedral_angle_3_deg17.925
r_dihedral_angle_1_deg7.623
r_scangle_it6.308
r_scbond_it4.016
r_mcangle_it2.437
r_angle_refined_deg2.177
r_mcbond_it1.347
r_chiral_restr0.163
r_bond_refined_d0.028
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1156
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing