2FQ1

Crystal structure of the two-domain non-ribosomal peptide synthetase EntB containing isochorismate lyase and aryl-carrier protein domains

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NF9	pdb entry 1NF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	10-15% mePEG5000, 0.8M MgCl2, 10% ethylene glycol, 50mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.889	α = 90
b = 82.331	β = 90
c = 164.73	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Max-Flux Confocal Mirrors	2004-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	2.3	25	96.3	0.063	15.5	3.8	31192	30038			47.8

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	2.3	2.38	80		0.341			2423

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1NF9	2.3	25	31509	29972	1545	95.12	0.189	0.189	0.186	0.241	RANDOM	45.001

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]
3.1			0.15		-3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.024
r_dihedral_angle_4_deg	18.551
r_dihedral_angle_3_deg	15.434
r_dihedral_angle_1_deg	5.562
r_scangle_it	5.162
r_mcangle_it	4.44
r_scbond_it	3.995
r_mcbond_it	3.28
r_angle_refined_deg	1.245
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.024
r_dihedral_angle_4_deg	18.551
r_dihedral_angle_3_deg	15.434
r_dihedral_angle_1_deg	5.562
r_scangle_it	5.162
r_mcangle_it	4.44
r_scbond_it	3.995
r_mcbond_it	3.28
r_angle_refined_deg	1.245
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.151
r_symmetry_vdw_refined	0.143
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4418
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	14

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	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 R01GM157729.