3H3C | pdb_00003h3c

Crystal structure of PYK2 in complex with Sulfoximine-substituted trifluoromethylpyrimidine analog

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, 0.1M bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.281	α = 90
b = 92.83	β = 92.64
c = 42.843	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	IMAGE PLATE	RIGAKU RAXIS IV++		2005-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.542

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	50		0.081	10.1	2.8		19055		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)
	2	2.07			0.496	2.03	2.6	1852

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	2	30	18043	975	96.55	0.22484	0.22235	0.22	0.27324	0.27	RANDOM	39.514

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]
-0.85		-0.2	-0.91		1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.924
r_scangle_it	4.501
r_scbond_it	2.813
r_mcangle_it	2.032
r_angle_refined_deg	1.629
r_mcbond_it	1.103
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.924
r_scangle_it	4.501
r_scbond_it	2.813
r_mcangle_it	2.032
r_angle_refined_deg	1.629
r_mcbond_it	1.103
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.126
r_symmetry_hbond_refined	0.047
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2134
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	56

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.