4NHD

Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in complex with Coenzyme A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GYO	PDB ENTRY 2GYO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		289	0.2M calcium chloride, 20%PEG3350, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.449	α = 90
b = 100.248	β = 90
c = 132.763	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	100	IMAGE PLATE	MAR scanner 300 mm plate	MIRRORS	2013-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9792	APS	21-ID-G

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	1.78	50	97.6	0.091	25.2	6.8		125028		-3	19.6

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	1.78	1.81	87.8		0.817	2	5.4	5576

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	PDB ENTRY 2GYO	1.78	50	124893	6293	98	0.1715	0.1702	0.1957	RANDOM	26.2697

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]
-0.67			-1.44		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.561
r_dihedral_angle_4_deg	16.302
r_dihedral_angle_3_deg	11.484
r_dihedral_angle_1_deg	5.751
r_angle_refined_deg	1.671
r_mcangle_it	1.66
r_angle_other_deg	1.067
r_mcbond_it	1.026
r_mcbond_other	1.026
r_chiral_restr	0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.561
r_dihedral_angle_4_deg	16.302
r_dihedral_angle_3_deg	11.484
r_dihedral_angle_1_deg	5.751
r_angle_refined_deg	1.671
r_mcangle_it	1.66
r_angle_other_deg	1.067
r_mcbond_it	1.026
r_mcbond_other	1.026
r_chiral_restr	0.18
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9458
Nucleic Acid Atoms
Solvent Atoms	1262
Heterogen Atoms	201

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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.