7BY9

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Nicotinamide Adenine Dinucleotide (NAD)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	The crystal of wild-type gs-MDH prepared in 0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000 and 5 % 2-Methyl-2,4-pentanediol (MPD) was soaked into the cryo-protectant containing 2 mM OAA and 2 mM NAD+.

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.156	α = 90
b = 83.239	β = 93.42
c = 119.477	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	PIXEL	DECTRIS EIGER X 4M		2018-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

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	2.2	50	99	0.198	0.966	4	4.6		62899

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	2.26			0.535	0.913	1.6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7BY8	2.2	39.393	62624	3047	99.564	0.226	0.2235	0.2848	42.666

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]
-0.024		-0.034	0.034		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.676
r_dihedral_angle_3_deg	20.495
r_dihedral_angle_4_deg	16.038
r_dihedral_angle_1_deg	7.925
r_lrange_it	7.314
r_lrange_other	7.313
r_mcangle_it	5.537
r_mcangle_other	5.537
r_scangle_it	5.073
r_scangle_other	5.072
r_mcbond_it	4.203
r_mcbond_other	4.203
r_scbond_it	3.831
r_scbond_other	3.831
r_angle_refined_deg	1.694
r_angle_other_deg	1.188
r_symmetry_nbd_refined	0.273
r_nbd_other	0.234
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.206
r_symmetry_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_other	0.106
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9332
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	212

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing