7NM8

The crystal structure of the antimycin pathway standalone ketoreductase, AntM, in complex with NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OSP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298.15	0.1 M Tris, pH 8.5, 5% w/v PEG 8K, 20% v/v PEG 300, 10% v/v glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.223	α = 90
b = 92.223	β = 90
c = 113.751	γ = 120

Symmetry
Space Group	P 62 2 2

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 EIGER2 X 16M		2018-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.7	65.36	100	1	24.7	21.2		33683

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	1.7	1.73			0.958

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	4osp	1.7	65.36	32045	1638	99.953	0.2	0.1987	0.2242	38.772

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]
1.67	0.835		1.67		-5.416

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.557
r_dihedral_angle_4_deg	17.404
r_dihedral_angle_3_deg	12.985
r_dihedral_angle_1_deg	6.577
r_lrange_other	6.236
r_lrange_it	6.234
r_scangle_it	5.292
r_scangle_other	5.29
r_mcangle_it	4.077
r_mcangle_other	4.068
r_scbond_it	3.78
r_scbond_other	3.778
r_mcbond_it	3.305
r_mcbond_other	3.291
r_angle_other_deg	2.414
r_angle_refined_deg	1.657
r_symmetry_nbd_other	0.222
r_nbd_other	0.221
r_nbd_refined	0.218
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.124
r_symmetry_xyhbond_nbd_other	0.123
r_symmetry_nbd_refined	0.107
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.069
r_bond_other_d	0.036
r_gen_planes_other	0.013
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1810
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
PHASER	phasing