3UWK | pdb_00003uwk

Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa Thymidylate Kinase: from Hit to Lead Generation

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	The protein was mixed 1:1 with a reservoir solution containing 30% PEG 4000, 0.2M MgCl2, and 0.1 M Tris pH 7.5 - 8.5 and incubated at 295, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.341	α = 90
b = 118.063	β = 90
c = 41.918	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 210		2010-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1	APS	17-ID

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	1.9	62.87	99.7	0.069	18.7	3.7	29391	110874	2	2

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	1.9	1.97	100		0.443	2.6	3.7	2876

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.91	62.87	29391	27872	1489	99.45	0.19688	0.19688	0.19455	0.2	0.2424	0.24	RANDOM	28.215

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]
-0.88			-0.16		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.008
r_dihedral_angle_4_deg	23.638
r_dihedral_angle_1_deg	21.728
r_dihedral_angle_3_deg	16.157
r_scangle_it	6.707
r_scbond_it	4.655
r_mcangle_it	2.98
r_mcbond_it	2.077
r_angle_refined_deg	1.742
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.008
r_dihedral_angle_4_deg	23.638
r_dihedral_angle_1_deg	21.728
r_dihedral_angle_3_deg	16.157
r_scangle_it	6.707
r_scbond_it	4.655
r_mcangle_it	2.98
r_mcbond_it	2.077
r_angle_refined_deg	1.742
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.279
r_nbd_refined	0.24
r_chiral_restr	0.161
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.12
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3076
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	35

Software

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

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.