7BY8

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TL2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES (pH 7.5), 10 % polyethylene glycol (PEG) 6000, 5 % 2-Methyl-2,4-pentanediol (MPD)

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.682	α = 90
b = 108.679	β = 90
c = 146.643	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 PILATUS3 6M		2018-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	1.945	50	99.7	0.079	0.998	11.2	11.8		95978

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	1.95	1.98			0.596	0.835

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	3TL2	1.945	44.619	95909	4804	99.501	0.208	0.2059	0.2546	39.396

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			0.011		-0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.414
r_dihedral_angle_3_deg	16.167
r_dihedral_angle_4_deg	11.469
r_dihedral_angle_1_deg	7.007
r_lrange_other	6.356
r_lrange_it	6.35
r_scangle_other	5.282
r_scangle_it	5.281
r_mcangle_it	4.059
r_mcangle_other	4.059
r_scbond_it	3.535
r_scbond_other	3.533
r_mcbond_it	3.124
r_mcbond_other	3.124
r_angle_refined_deg	1.515
r_angle_other_deg	1.282
r_nbd_other	0.233
r_nbd_refined	0.195
r_symmetry_nbd_other	0.176
r_symmetry_nbd_refined	0.165
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.132
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.008
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	9290
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing