3G25

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	1:1 v/v protein solution [10mg/ml protein, 0.3M NaCl, 10mM Na Hepes pH 7.5), screen solution (0.2M Na dihydrogen Phosphate , 20% PEG 3350, 6% Glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.75	α = 90
b = 193.742	β = 103.6
c = 91.669	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	CCD	MARMOSAIC 300 mm CCD		2008-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.98400	APS	21-ID-D

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	1.9	50	100	0.081	15.6	3.9	168279	168279		-3	23.4

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)
1	1.9	1.93	100		0.494	2.9	3.8	8395

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EZW	1.9	44.81	159730	159730	8479	99.85	0.19529	0.19529	0.19266	0.24562	RANDOM	15.064

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]
4.41		0.58	-2.76		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.732
r_dihedral_angle_4_deg	14.063
r_dihedral_angle_3_deg	12.183
r_scangle_it	5.319
r_dihedral_angle_1_deg	4.128
r_scbond_it	3.723
r_mcangle_it	2.175
r_angle_refined_deg	1.679
r_mcbond_it	1.471
r_angle_other_deg	0.971

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.732
r_dihedral_angle_4_deg	14.063
r_dihedral_angle_3_deg	12.183
r_scangle_it	5.319
r_dihedral_angle_1_deg	4.128
r_scbond_it	3.723
r_mcangle_it	2.175
r_angle_refined_deg	1.679
r_mcbond_it	1.471
r_angle_other_deg	0.971
r_mcbond_other	0.547
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15703
Nucleic Acid Atoms
Solvent Atoms	1174
Heterogen Atoms	96

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.