7F8D | pdb_00007f8d

Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) G218Y mutant

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	20 mM Tris-HCl (pH 7.0), 12% PEG 8000, 0.2 M magnesium chloride, 2 mM oxaloacetic acid, 2 mM NAD

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.424	α = 90
b = 110.22	β = 90
c = 150.827	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	2.4	48.51	100	0.091	0.999	21.6	13.5		51272

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	2.4	2.47			0.39	0.973	7.7

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	2.4	48.509	51207	2625	99.975	0.184	0.1795	0.19	0.2579	0.25	50.407

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]
0.044			0.002		-0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.533
r_dihedral_angle_3_deg	17.58
r_dihedral_angle_4_deg	16.568
r_lrange_other	9.226
r_lrange_it	9.225
r_scangle_it	7.606
r_scangle_other	7.606
r_dihedral_angle_1_deg	7.182
r_mcangle_it	5.681
r_mcangle_other	5.681
r_scbond_it	5.39
r_scbond_other	5.389
r_mcbond_it	4.246
r_mcbond_other	4.245
r_angle_refined_deg	1.561
r_angle_other_deg	1.266
r_nbd_other	0.21
r_nbd_refined	0.201
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_bond_refined_d	0.009
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	9520
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	176

Software

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