4I4Z

Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with salicylyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EML

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294	0.15M ammonium acetate, 4% Tasmate, 0.1M Bis-tris, 15% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.21	α = 90
b = 139.21	β = 90
c = 220.981	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	100	CCD	ADSC QUANTUM 315r		2011-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97	SSRF	BL17U

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	2	44.67	99.65			159143	158586		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	99.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4EML	2	44.67	158586	8387	99.65	0.19959	0.19847	0.22087	RANDOM	34.601

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]
0.9	0.9		0.9		-2.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.539
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_1_deg	5.29
r_angle_refined_deg	1.423
r_angle_other_deg	1.087
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.539
r_dihedral_angle_4_deg	18.603
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_1_deg	5.29
r_angle_refined_deg	1.423
r_angle_other_deg	1.087
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19113
Nucleic Acid Atoms
Solvent Atoms	883
Heterogen Atoms	563

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM157729.