6T5X | pdb_00006t5x

Crystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 10 mM NADPH (added to the protein solution) Cryoprotection of the crystals: dipping them in 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 26% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.43	α = 90
b = 71.144	β = 94.42
c = 81.366	γ = 90

Symmetry
Space Group	I 1 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	PIXEL	DECTRIS PILATUS3 S 6M	toroidal mirror	2016-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.5	58.49	95.9	0.025	0.032	0.02	0.999	18.3	2.3		67342		2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	97.4		0.387	0.491	0.335	0.843	2.5	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4AFN	1.5	58.21	63956	3434	95.69	0.1602	0.1588	0.1598	0.185	0.1645	RANDOM	25.223

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]
0.39		-0.34	1.15		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.263
r_dihedral_angle_4_deg	14.5
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_1_deg	5.612
r_angle_refined_deg	1.479
r_angle_other_deg	0.934
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.263
r_dihedral_angle_4_deg	14.5
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_1_deg	5.612
r_angle_refined_deg	1.479
r_angle_other_deg	0.934
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3554
Nucleic Acid Atoms
Solvent Atoms	456
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	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.