3RWQ | pdb_00003rwq

Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.213	α = 90
b = 123.213	β = 90
c = 47.424	γ = 120

Symmetry
Space Group	P 32 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	93	IMAGE PLATE	RIGAKU RAXIS		2006-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.55	50	95.8	0.141	13.69	5.99	13179	13175	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.64	95.6		0.459	2.56	3.9	1306

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	2.55	50	12514	12514	659	95.87	0.19633	0.19633	0.19332	0.1942	0.2555	0.256	RANDOM	42.118

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]
0.8	0.4		0.8		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.615
r_dihedral_angle_4_deg	25.961
r_dihedral_angle_3_deg	17.832
r_dihedral_angle_1_deg	6.366
r_scangle_it	2.996
r_scbond_it	1.963
r_angle_refined_deg	1.553
r_mcangle_it	1.475
r_mcbond_it	0.884
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.615
r_dihedral_angle_4_deg	25.961
r_dihedral_angle_3_deg	17.832
r_dihedral_angle_1_deg	6.366
r_scangle_it	2.996
r_scbond_it	1.963
r_angle_refined_deg	1.553
r_mcangle_it	1.475
r_mcbond_it	0.884
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.275
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.189
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2313
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	83

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.