3BZM

Crystal Structure of Open form of Menaquinone-Specific Isochorismate Synthase, MenF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	8	298	well solution: 0.2M sodium citrate, 6% glycerol, 8% PEG 3350, 5mM chorismic acid. protein solution: 50mM Tris, 5 mM magnesium chloride, 1 mM DTT, pH 7.6, 20 mg/mL. Drops were equal volumes well and protein., sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.37	α = 90
b = 72.37	β = 90
c = 164.01	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	IMAGE PLATE	RIGAKU RAXIS IV++		2007-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.95	19.67	98.1	0.064	14.7	7.97		36355

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)
	1.95	2.02	84.8		0.474	2.6	4.61	3084

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	19.67	35738	1804	96.43	0.248	0.245	0.308	RANDOM	48.543

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]
1.09	0.54		1.09		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.792
r_dihedral_angle_3_deg	20.588
r_dihedral_angle_4_deg	15.875
r_dihedral_angle_1_deg	7.575
r_scangle_it	3.785
r_scbond_it	2.679
r_angle_refined_deg	1.975
r_mcangle_it	1.794
r_mcbond_it	1.108
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.792
r_dihedral_angle_3_deg	20.588
r_dihedral_angle_4_deg	15.875
r_dihedral_angle_1_deg	7.575
r_scangle_it	3.785
r_scbond_it	2.679
r_angle_refined_deg	1.975
r_mcangle_it	1.794
r_mcbond_it	1.108
r_nbtor_refined	0.311
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.149
r_symmetry_hbond_refined	0.133
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3432
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	13

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

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.