4IQL | pdb_00004iql

Crystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase II (FabK) with cofactors NADPH and FMN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6J	PDB ENTRY 2Z6J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	20% PEG 3350, 0.2M sodium formate, 5mM MOPS (pH 7.0), 1mM DTT. 3uL(protein stock):3uL(Index 90):1uL Seed stock. (Seed Stock From: 10% PEG 3350, 0.15M Na Citrate pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.652	α = 90
b = 86.652	β = 90
c = 150.505	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	CCD	RAYONIX MX-225		2012-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.938	20	99.5	0.134	0.134	15.2	7.1	90851	90851	1	1	20.56

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	1.938	2.05	97.5		0.538	4.19	6.8	14235

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Z6J	1.938	20	47951	45527	2424	99.71	0.16331	0.16331	0.161	0.16	0.20695	0.2	RANDOM	13.324

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]
-0.19			0.4		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.272
r_dihedral_angle_4_deg	18.473
r_dihedral_angle_3_deg	13.33
r_dihedral_angle_1_deg	12.864
r_scangle_it	6.401
r_scbond_it	3.96
r_mcangle_it	2.166
r_angle_refined_deg	1.606
r_mcbond_it	1.279
r_chiral_restr	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.272
r_dihedral_angle_4_deg	18.473
r_dihedral_angle_3_deg	13.33
r_dihedral_angle_1_deg	12.864
r_scangle_it	6.401
r_scbond_it	3.96
r_mcangle_it	2.166
r_angle_refined_deg	1.606
r_mcbond_it	1.279
r_chiral_restr	0.123
r_bond_refined_d	0.017
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4638
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	190

Software

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