2EUA

Structure and Mechanism of MenF, the Menaquinone-Specific Isochorismate Synthase from Escherichia Coli

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.8 M potassium sodium tartrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.408	α = 90
b = 146.408	β = 90
c = 125.6	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC QUANTUM 4		2004-07-24	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 4		2004-10-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.25360	NSLS	X26C
2	SYNCHROTRON	NSLS BEAMLINE X26C	0.9745, 0.97971	NSLS	X26C

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	2.5	50	99.1	0.099				47401	2	2

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)
	2.5	2.54	85.4	85.4	0.543

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	MAD	THROUGHOUT	2.5	25	47073	44680	2393	98.65	0.232	0.232	0.229	0.276	RANDOM	57.033

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]
-0.05			-0.05		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_3_deg	20.43
r_dihedral_angle_4_deg	16.579
r_dihedral_angle_1_deg	8.959
r_scangle_it	2.206
r_angle_refined_deg	1.592
r_scbond_it	1.401
r_mcangle_it	0.93
r_mcbond_it	0.541
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_3_deg	20.43
r_dihedral_angle_4_deg	16.579
r_dihedral_angle_1_deg	8.959
r_scangle_it	2.206
r_angle_refined_deg	1.592
r_scbond_it	1.401
r_mcangle_it	0.93
r_mcbond_it	0.541
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.26
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.221
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6693
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.