5TR3

2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 13.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: Classics II(F10), 0.2M Sodim chloride, 0.01M Tris HCl (pH 6.5), 25% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.886	α = 90
b = 132.113	β = 90
c = 158.132	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	MARMOSAIC 300 mm CCD	C(111)	2016-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	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	2.5	30	99.9	0.075	0.075	20.1	4.9		42116		-3	51.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	100		0.632	0.837	2.6	4.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3LAD	2.5	29.42	40007	2044	99.77	0.22729	0.2254	0.26422	RANDOM	60.399

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]
-1.47			7.17		-5.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.201
r_dihedral_angle_4_deg	14.204
r_dihedral_angle_3_deg	10.771
r_long_range_B_refined	5.665
r_long_range_B_other	5.651
r_scangle_other	2.822
r_mcangle_it	2.763
r_mcangle_other	2.763
r_dihedral_angle_1_deg	1.998
r_scbond_it	1.758
r_scbond_other	1.754
r_mcbond_it	1.733
r_mcbond_other	1.732
r_angle_refined_deg	1.459
r_angle_other_deg	0.877
r_chiral_restr	0.081
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6924
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing