3DZV

Crystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinase (NP_816404.1) from ENTEROCOCCUS FAECALIS V583 at 2.57 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	1.6M ammonium sulfate, 0.1M citric acid pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.15	70.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.705	α = 90
b = 181.705	β = 90
c = 181.705	γ = 90

Symmetry
Space Group	I 21 3

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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-06-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97954,0.97968	SSRL	BL9-2

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	2.57	29.476	99.9	0.168	0.168	10	5.6		31815			50.24

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)
	2.57	2.64	100		0.976	0.976	1.6	5.6	2335

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.57	29.476	31794	1604	99.85	0.177	0.175	0.204	RANDOM	32.195

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.146
r_dihedral_angle_4_deg	18.729
r_dihedral_angle_3_deg	16.553
r_scangle_it	7.324
r_dihedral_angle_1_deg	6.061
r_scbond_it	5.261
r_mcangle_it	2.582
r_mcbond_it	1.633
r_angle_refined_deg	1.487
r_angle_other_deg	0.931
r_mcbond_other	0.248
r_nbd_refined	0.223
r_symmetry_vdw_other	0.209
r_nbd_other	0.187
r_nbtor_refined	0.182
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.12
r_nbtor_other	0.088
r_chiral_restr	0.072
r_bond_refined_d	0.015
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4029
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction