5J5Z | pdb_00005j5z

Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	293.15	reservoir solution: 1.6 M NaH2PO4/K2HPO4 buffer, pH 8.1 (K2HPO4 was titrated with NaH2PO4 to pH 8.1)

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.035	α = 90
b = 168.939	β = 90
c = 61.279	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		2015-05-06	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)	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	1.84	48.38	98.1	10.78	4.54		105160			36.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.95	97.4		0.87

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	1ZMD	1.84	48.38	103058	2101	98.1	0.1823	0.1814	0.19	0.2261	0.23	RANDOM	39.357

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]
-0.71			-0.42		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.234
r_dihedral_angle_3_deg	15.353
r_dihedral_angle_4_deg	14.945
r_dihedral_angle_1_deg	6.661
r_mcangle_it	2.643
r_angle_refined_deg	2.427
r_mcbond_it	1.728
r_mcbond_other	1.722
r_angle_other_deg	1.184
r_chiral_restr	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.234
r_dihedral_angle_3_deg	15.353
r_dihedral_angle_4_deg	14.945
r_dihedral_angle_1_deg	6.661
r_mcangle_it	2.643
r_angle_refined_deg	2.427
r_mcbond_it	1.728
r_mcbond_other	1.722
r_angle_other_deg	1.184
r_chiral_restr	0.154
r_bond_refined_d	0.027
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7123
Nucleic Acid Atoms
Solvent Atoms	499
Heterogen Atoms	140

Software

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

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.