6HG8

Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	293.15	protein in: 100 mM Tris,150 mM NaCl, 1 mM EDTA, pH 8.0 reservoir solution: 2 M (NH4)2SO4, 2 v/v% PEG-400, 0.1 M HEPES (pH 6.9) volume ratio: 1

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.913	α = 90
b = 169.497	β = 90
c = 61.401	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M		2017-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.76	48.4	93	0.141	0.998	9.5	6.8		114691

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	1.76	1.86	71.2		0.255	0.365	0.59	6.7

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	1ZMD	1.76	30	111625	2083	92.19	0.1883	0.18737	0.2374	RANDOM	33.417

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]
0.87			-2.95		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.678
r_dihedral_angle_3_deg	15.39
r_dihedral_angle_4_deg	11.847
r_long_range_B_refined	7.407
r_long_range_B_other	7.406
r_dihedral_angle_1_deg	6.636
r_scangle_other	5.779
r_scbond_it	3.927
r_scbond_other	3.926
r_mcangle_it	3.457
r_mcangle_other	3.457
r_mcbond_it	2.632
r_mcbond_other	2.63
r_angle_refined_deg	1.893
r_angle_other_deg	1.036
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.003
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	7072
Nucleic Acid Atoms
Solvent Atoms	904
Heterogen Atoms	169

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data scaling
XDS	data reduction
MOLREP	phasing