2X0J | pdb_00002x0j

2.8 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH ETHENO-NAD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4		INITIAL PROTEIN DROPLET: 22 MG/ML PROTEIN, 10 MM ETHENO-NAD RESERVOIR: 1.6 % (W/V) POLYETHYLENE GLYCOL 8000, 0.8 M LISO4 DROPLET: EQUAL VOLUMES OF INITIAL PROTEIN DROPLET AND RESERVOIR, pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
3.57	62.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.99	α = 90
b = 112.99	β = 90
c = 70.6	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARRESEARCH	TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.79	35.8	90.9	0.05	43.5	15.5		10861		0.5	67.74

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.89	71		0.15	12.7	10.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	OTHER	2.786	35.731	2.21	10819	585	90.88	0.167	0.164	0.17	0.2165	0.22	73.59

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]
-12.0764			-12.0764		24.1527

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	25.57
f_angle_d	1.249
f_chiral_restr	0.092
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2237
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	51

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
BIOMOL	data scaling

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.