6CMZ | pdb_00006cmz

2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	Protein: 8.0 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD; Screen: PACT (D1), 0.1M MMT buffer pH 4.0, 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.565	α = 90
b = 107.246	β = 106.09
c = 105.427	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	MARMOSAIC 300 mm CCD	C(111)	2018-02-06	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)	Rrim I (All)	Rpim I (All)	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	30	100	0.109	0.109	0.124	0.059	13.2	4.4		79190		-3	42.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	100		0.791	0.791	0.909	0.443	0.624	1.9	4.1

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	1LVL	2.3	29.21	75207	3962	99.72	0.20144	0.19868	0.2	0.2532	0.25	RANDOM	50.659

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]
-1.2		1.03	0.44		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.935
r_dihedral_angle_4_deg	12.459
r_dihedral_angle_3_deg	9.891
r_long_range_B_refined	5.389
r_long_range_B_other	5.37
r_scangle_other	3.031
r_mcangle_it	2.43
r_mcangle_other	2.43
r_dihedral_angle_1_deg	2.077
r_scbond_it	1.855
r_scbond_other	1.855
r_angle_refined_deg	1.466
r_mcbond_it	1.458
r_mcbond_other	1.458
r_angle_other_deg	0.891
r_chiral_restr	0.082
r_gen_planes_refined	0.022
r_gen_planes_other	0.019
r_bond_refined_d	0.008
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	13576
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	432

Software

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