2XPB

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 = 68.668α = 90
b = 68.668β = 90
c = 79.477γ = 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
123097.10.095.82.21146432
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)
122.0897.50.461.52.15

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 3KCE259.441388673696.910.225440.222580.27699RANDOM29.074
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]
0.760.380.76-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg19.308
r_dihedral_angle_3_deg18.22
r_dihedral_angle_1_deg7.63
r_scangle_it5.052
r_scbond_it3.206
r_mcangle_it2.037
r_angle_refined_deg1.832
r_mcbond_it1.145
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.636
r_dihedral_angle_4_deg19.308
r_dihedral_angle_3_deg18.22
r_dihedral_angle_1_deg7.63
r_scangle_it5.052
r_scbond_it3.206
r_mcangle_it2.037
r_angle_refined_deg1.832
r_mcbond_it1.145
r_chiral_restr0.126
r_bond_refined_d0.022
r_gen_planes_refined0.009
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 Atoms104
Heterogen Atoms35

Software

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