3PFD | pdb_00003pfd

Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion SAD MR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JQI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M phosphate citrate pH 4.2, crystal tracking ID 216661c1-1MNaI, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.43	α = 90
b = 114.55	β = 92.13
c = 92.77	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RIGAKU SATURN 944		2010-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.1	50	99.3	0.132	11.74	7.2		89991		-3	24.921

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	2.1	2.15	91.2		0.531	3.5	6.2	6704

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	SAD WITH MR	THROUGHOUT	1jqi	2.1	50	89872	4507	99.18	0.171	0.1691	0.17	0.2068	0.21	RANDOM	21.3214

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]
-0.57		-0.36	-0.09		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.866
r_dihedral_angle_4_deg	17.561
r_dihedral_angle_3_deg	13.581
r_dihedral_angle_1_deg	5.346
r_scangle_it	3.262
r_scbond_it	2.033
r_angle_refined_deg	1.393
r_mcangle_it	1.17
r_mcbond_it	0.664
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.866
r_dihedral_angle_4_deg	17.561
r_dihedral_angle_3_deg	13.581
r_dihedral_angle_1_deg	5.346
r_scangle_it	3.262
r_scbond_it	2.033
r_angle_refined_deg	1.393
r_mcangle_it	1.17
r_mcbond_it	0.664
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10870
Nucleic Acid Atoms
Solvent Atoms	623
Heterogen Atoms	321

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
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.