3MBJ

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	35.00% 2-methyl-2,4-pentanediol, 0.20M lithium sulfate, 0.1M MES pH 6.0, Additive: 0.001M zinc chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.627	α = 90
b = 161.627	β = 90
c = 76.138	γ = 120

Symmetry
Space Group	H 3 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-07-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97916,0.97871	SSRL	BL11-1

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	2.1	29.591	100	0.137	0.137	10.7	5.7		22278			28.253

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)
1	2.1	2.15	100		0.838	0.838	0.9	5.7	1645

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	2.1	29.591	22278	1137	99.95	0.173	0.171	0.21	RANDOM	23.496

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]
-1.79	-0.89		-1.79		2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.374
r_dihedral_angle_4_deg	20.543
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_1_deg	6.686
r_scangle_it	3.698
r_scbond_it	2.488
r_angle_refined_deg	1.615
r_mcangle_it	1.396
r_angle_other_deg	0.941
r_mcbond_it	0.759

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.374
r_dihedral_angle_4_deg	20.543
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_1_deg	6.686
r_scangle_it	3.698
r_scbond_it	2.488
r_angle_refined_deg	1.615
r_mcangle_it	1.396
r_angle_other_deg	0.941
r_mcbond_it	0.759
r_mcbond_other	0.194
r_chiral_restr	0.096
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2257
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing
SHELXD	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 R01GM133198.