1WVY | pdb_00001wvy

Crystal structures of kinase domain of DAP kinase in complex with small molecular inhibitors

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	283	Tris-HCl, PEG400, PEG8000, glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.911	α = 90
b = 113.162	β = 90
c = 50.658	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2002-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	0.7000	SPring-8	BL40B2

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	2.8	42.63	99.9	0.11			11737	11722	1	2	46.3

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)
	2.8	2.95	99.7		0.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	10	1	11399	10212	1172	89.6	0.222	0.222	0.2135	0.2735	RANDOM	42.8

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]
0.13			-1.47		1.34

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.9
c_scangle_it	3.08
c_mcangle_it	2.46
c_scbond_it	1.98
c_mcbond_it	1.4
c_angle_deg	1.2
c_improper_angle_d	0.73
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2217
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	35

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	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.