2X8E | pdb_00002x8e

Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X8D	PDB ENTRY 2X8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		HANGING DROP 3UL PLUS 3UL PROTEIN: 7 MG/ML, 25MM TRIS PH7.5, 500MM NACL, 5% GLYCEROL, 5MM DTT, 2MM COMPOUND WELL: 12-16% (W/V) PEG3350, 100-200MM AMMONIUM SULPHATE, 2% (V/V) GLYCEROL AND 100 MM SODIUM CACODYLATE PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.055	α = 90
b = 65.858	β = 101.73
c = 54.468	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH SX-165		2002-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	2.5	16.55	72.5	0.11	5.4	2.6		7559		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	2.5	2.64	26.3		0.27	2	1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2X8D	2.5	16.51	7187	372	69.68	0.23547	0.23185	0.24	0.30865	0.32	RANDOM	42.257

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]
-3.33		1.81	1.97		2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.042
r_dihedral_angle_4_deg	21.374
r_dihedral_angle_3_deg	18.202
r_dihedral_angle_1_deg	6.776
r_scangle_it	1.982
r_angle_refined_deg	1.531
r_scbond_it	1.223
r_mcangle_it	0.951
r_angle_other_deg	0.93
r_mcbond_it	0.516
r_mcbond_other	0.079
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_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	2054
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing