3NF4 | pdb_00003nf4

Crystal structure of acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to flavin adenine dinucleotide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DVL	2dvl molecule a

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	69.7 mg/mL protein against PACT screen condition e11, 0.2 M Na Citrate, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 215726e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.65	α = 90
b = 99.23	β = 90
c = 171.49	γ = 90

Symmetry
Space Group	I 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	ADSC QUANTUM 315r		2010-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	2.35	50	98.8	0.063	22.1	8.6	34384	33958		-3	44.057

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	2.35	2.41	96.9		0.339	6.6	8.8	2504

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	2dvl molecule a	2.35	19.69	33892	1697	98.57	0.194	0.191	0.2	0.24	0.21	RANDOM	59.617

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]
-3.08			-0.35		3.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.436
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	16.414
r_dihedral_angle_1_deg	5.445
r_scangle_it	3.324
r_scbond_it	2.047
r_angle_refined_deg	1.453
r_mcangle_it	1.219
r_mcbond_it	0.639
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.436
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	16.414
r_dihedral_angle_1_deg	5.445
r_scangle_it	3.324
r_scbond_it	2.047
r_angle_refined_deg	1.453
r_mcangle_it	1.219
r_mcbond_it	0.639
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5447
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.