2XPB

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KCE	PDB ENTRY 3KCE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	2.2M AMMONIUM SULPHATE, 0.1M HEPES BUFFER, 1% PEG 400, 5MM DTT, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.668	α = 90
b = 68.668	β = 90
c = 79.477	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	30	97.1	0.09	5.8	2.21		14643		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.08	97.5		0.46	1.5	2.15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3KCE	2	59.44	13886	736	96.91	0.22544	0.22258	0.27699	RANDOM	29.074

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]
0.76	0.38		0.76		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.636
r_dihedral_angle_4_deg	19.308
r_dihedral_angle_3_deg	18.22
r_dihedral_angle_1_deg	7.63
r_scangle_it	5.052
r_scbond_it	3.206
r_mcangle_it	2.037
r_angle_refined_deg	1.832
r_mcbond_it	1.145
r_chiral_restr	0.126
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
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 Atoms	Number
Protein Atoms	1156
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing