3B96 | pdb_00003b96

Structural Basis for Substrate Fatty-Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1 M HEPES, 17.6% PEG 2000, 0.047 M MgCl2, 5% glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.616	α = 90
b = 107.879	β = 90
c = 149.776	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2006-05-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD			2006-05-14	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD			2006-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.5419
2	SYNCHROTRON	APS BEAMLINE 19-ID	1.0083	APS	19-ID
3	SYNCHROTRON	APS BEAMLINE 5ID-B	1.1405	APS	5ID-B

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
1,2,3	1.91	50	98.8	0.079	15.2	7.6		46776

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)
	1.91	1.98	98.4		0.532		6.7	4630

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIRAS	THROUGHOUT	1.91	30.69	46738	2371	98.65	0.162	0.159	0.16	0.216	0.22	RANDOM	24.049

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]
0.1			-0.06		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.3
r_dihedral_angle_4_deg	14.36
r_dihedral_angle_3_deg	14.295
r_scangle_it	9.717
r_scbond_it	7.019
r_dihedral_angle_1_deg	6.034
r_mcangle_it	4.221
r_mcbond_it	3.728
r_angle_refined_deg	1.353
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.3
r_dihedral_angle_4_deg	14.36
r_dihedral_angle_3_deg	14.295
r_scangle_it	9.717
r_scbond_it	7.019
r_dihedral_angle_1_deg	6.034
r_mcangle_it	4.221
r_mcbond_it	3.728
r_angle_refined_deg	1.353
r_nbtor_refined	0.309
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.214
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.113
r_bond_refined_d	0.014
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4225
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	76

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.