1JXH | pdb_00001jxh

4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	magnesium sulfate, MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2	VAPOR DIFFUSION, HANGING DROP	7	291	MgSO4, MES, 1,6-hexanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.724	α = 90
b = 77.724	β = 90
c = 183.419	γ = 90

Symmetry
Space Group	P 41 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 4	Mirrors	2000-06-22	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	CUSTOM-MADE	Mirrors	1999-12-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.909	CHESS	A1
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.9795, 0.9793, 0.9537	APS	19-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
1,2	2.3	25	99.3	0.063	8.3	7	38761	38761

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	2.3	25	25741	25741	2604		0.235	0.23	0.272	0.27	random	47.7103

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]
-8.353			-8.353		16.706

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.95
c_angle_deg	1.24
c_improper_angle_d	0.8
c_bond_d	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3764
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	20

Software

Software
Software Name	Purpose
MLPHARE	phasing
CNS	refinement
MOSFLM	data reduction
SCALEPACK	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.