6ITK

Crystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TVO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG 3350, HEPES, MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.931	α = 90
b = 116.94	β = 95.31
c = 66.003	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 270		2016-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	77.08	96.3	0.123	18	2.7		50050

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	2.03	93		0.39	0.792

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	4TVO	2	26.73	47560	2490	95.87	0.1918	0.1898	0.2291	RANDOM	24.369

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]
4.31		0.27	-0.66		-3.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.003
r_dihedral_angle_4_deg	21.702
r_dihedral_angle_3_deg	14.466
r_dihedral_angle_1_deg	7.162
r_angle_refined_deg	1.624
r_angle_other_deg	1.332
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.003
r_dihedral_angle_4_deg	21.702
r_dihedral_angle_3_deg	14.466
r_dihedral_angle_1_deg	7.162
r_angle_refined_deg	1.624
r_angle_other_deg	1.332
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4774
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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 R01GM133198.