3CWC

Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	287	10% PEG 3000, 0.1 M Phosphate-citrate buffer, 0.2 M Sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.733	α = 90
b = 59.549	β = 106.01
c = 103.605	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	ADSC QUANTUM 315		2008-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	APS	19-ID

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	2.23	49.81	99.9	0.075	31.4	5.5	36765	36765			49.8

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	2.23	2.27	98.4		0.622	2.09	4.4	1789

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.23	49.81	36722	36722	1834	99.6	0.191	0.191	0.188	0.237	RANDOM	38.093

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]
-1.06		-1.21	0.96		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.028
r_dihedral_angle_4_deg	21.095
r_dihedral_angle_3_deg	19.231
r_dihedral_angle_1_deg	6.402
r_scangle_it	3.273
r_scbond_it	2.206
r_angle_refined_deg	1.547
r_mcangle_it	1.398
r_mcbond_it	1.078
r_angle_other_deg	1.015
r_symmetry_vdw_other	0.285
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.208
r_nbd_other	0.203
r_mcbond_other	0.185
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.168
r_symmetry_hbond_refined	0.143
r_nbtor_other	0.093
r_chiral_restr	0.084
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5405
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing