1K47 | pdb_00001k47

Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	sodium dihydrogen phosphate, potassium dihydrogen phosphate, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 231.606	α = 90
b = 231.606	β = 90
c = 88.587	γ = 120

Symmetry
Space Group	P 63

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	BRANDEIS - B4	27-pole hybrid wiggler and vertical focusing mirror	2001-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9792	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	20	98.3	0.082	0.082	24.1	6.8	202265	198856	1	1	46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	92.3		0.409	0.409	2.5		18706

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	Single anomalous scattering	THROUGHOUT	2.42	20	192349	192349	18573	95	0.217	0.217	0.215	0.22	0.257	0.26	random

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]
1.528	-5.718		1.528		-3.055

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	4.025
c_scbond_it	3.162
c_mcangle_it	2.272
c_mcbond_it	1.348
c_angle_deg	1.319
c_bond_d	0.0066

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15000
Nucleic Acid Atoms
Solvent Atoms	779
Heterogen Atoms

Software

Software
Software Name	Purpose
SnB	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	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.