4IV6

X-ray crystal structure of an isovaleryl-CoA dehydrogenase from Mycobacterium smegmatis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	JCSG+ well B10: 0.2 M magnesium chloride, 0.1 M sodium cacodylate, pH 6.50, 50% PEG200, 21.63 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.82	α = 90
b = 105.82	β = 90
c = 169.49	γ = 90

Symmetry
Space Group	P 41 21 2

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		2012-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97740	ALS	5.0.1

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	50	98.1	0.104	13.73		65695	64445		-3	26.487

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	2.05	99.4		0.551	3.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2	45.62	65695	64429	3267	98.21	0.1513	0.1495	0.1848	RANDOM	22.593

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]
-0.21			-0.21		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.133
r_dihedral_angle_4_deg	15.82
r_dihedral_angle_3_deg	13.37
r_dihedral_angle_1_deg	5.62
r_angle_refined_deg	1.441
r_mcangle_it	1.202
r_angle_other_deg	0.815
r_mcbond_it	0.74
r_mcbond_other	0.738
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.133
r_dihedral_angle_4_deg	15.82
r_dihedral_angle_3_deg	13.37
r_dihedral_angle_1_deg	5.62
r_angle_refined_deg	1.441
r_mcangle_it	1.202
r_angle_other_deg	0.815
r_mcbond_it	0.74
r_mcbond_other	0.738
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5809
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	106

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.