7X1L | pdb_00007x1l

Malate dehydrogenase from Geobacillus stearothermophilus (gs-MDH) delta E311 mutant complexed with Nicotinamide Adenine Dinucleotide (NAD+)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BY8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M CHES (pH 8.8), 20 % (w/v) PEG 8000, 2 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 242.85	α = 90
b = 82.724	β = 98.588
c = 136.703	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	PIXEL	DECTRIS EIGER X 16M		2021-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.28	48.633	99.8	0.999	7.8	3.9		122192

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.32			0.997		4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7BY8	2.28	48.633	122190	6081	99.812	0.235	0.2329	0.2357	0.28	0.2786	64.49

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]
0.017		-0.003	-0.004		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.294
r_dihedral_angle_3_deg	18.25
r_dihedral_angle_4_deg	17.931
r_lrange_other	10.515
r_lrange_it	10.512
r_scangle_it	8.554
r_scangle_other	8.554
r_mcangle_it	7.15
r_mcangle_other	7.15
r_dihedral_angle_1_deg	6.993
r_scbond_it	5.92
r_scbond_other	5.92
r_mcbond_it	5.386
r_mcbond_other	5.386
r_angle_refined_deg	1.5
r_angle_other_deg	1.22
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_xyhbond_nbd_other	0.207
r_nbd_other	0.204
r_nbd_refined	0.195
r_symmetry_nbd_other	0.176
r_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.155
r_symmetry_nbd_refined	0.149
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.065
r_xyhbond_nbd_other	0.032
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	13820
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	264

Software

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