7BYA

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) complexed with Oxaloacetic Acid (OAA) and Adenosine 5'-Diphosphoribose (APR)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-HCl (pH 7.0), 16 % PEG 2000 MME, 2 mM OAA, and 2 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.327	α = 90
b = 103.22	β = 90
c = 150.79	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-05-21	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	49.16	100	0.111	0.999	21.8	27.6		66776

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	2.25			0.441	0.99	8.1

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	49.159	66701	3434	99.988	0.183	0.1804	0.2299	48.842

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]
0.002					-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.936
r_dihedral_angle_3_deg	15.875
r_dihedral_angle_4_deg	15.535
r_lrange_other	6.924
r_lrange_it	6.923
r_dihedral_angle_1_deg	6.886
r_scangle_it	5.857
r_scangle_other	5.856
r_mcangle_it	4.542
r_mcangle_other	4.542
r_scbond_it	4.078
r_scbond_other	4.076
r_mcbond_it	3.536
r_mcbond_other	3.534
r_angle_refined_deg	1.469
r_angle_other_deg	1.266
r_symmetry_xyhbond_nbd_refined	0.316
r_nbd_refined	0.196
r_nbd_other	0.183
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.077
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9375
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	153

Software

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