1Q52

Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	dioxane, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.375	α = 90
b = 139.432	β = 97.29
c = 142.027	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 4		2002-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50					312176

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	50	312176	15654	97.43	0.19749	0.19749	0.19538	0.21861	RANDOM	33.313

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]
-0.1			0.06		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.943
r_scangle_it	4.804
r_scbond_it	3.098
r_mcangle_it	1.981
r_angle_refined_deg	1.794
r_mcbond_it	1.194
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.943
r_scangle_it	4.804
r_scbond_it	3.098
r_mcangle_it	1.981
r_angle_refined_deg	1.794
r_mcbond_it	1.194
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.16
r_chiral_restr	0.135
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25503
Nucleic Acid Atoms
Solvent Atoms	2984
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
BEAST	phasing
COMO	phasing

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.