7NM7 | pdb_00007nm7

The crystal structure of the antimycin pathway standalone ketoreductase, AntM

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 citrate phosphate buffer, pH 4.2, 0.2 M NaCl, and 10% w/v PEG 3K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.897	α = 90
b = 87.897	β = 90
c = 116.262	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	2.1	63.69	99.9	0.997	7.8	9		16855

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	2.1	2.16			0.752

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	4osp	2.1	63.69	16085	770	99.826	0.216	0.2135	0.2136	0.2727	0.2728	43.35

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]
2.008	1.004		2.008		-6.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.224
r_dihedral_angle_4_deg	17.358
r_dihedral_angle_3_deg	14.022
r_lrange_other	11.723
r_lrange_it	11.717
r_dihedral_angle_1_deg	7.279
r_scangle_it	6.142
r_scangle_other	6.134
r_mcangle_it	4.901
r_mcangle_other	4.9
r_scbond_it	4.336
r_scbond_other	4.336
r_mcbond_it	3.667
r_mcbond_other	3.651
r_angle_other_deg	2.516
r_angle_refined_deg	1.65
r_symmetry_xyhbond_nbd_refined	0.551
r_nbd_other	0.228
r_symmetry_nbd_other	0.222
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.206
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.069
r_symmetry_xyhbond_nbd_other	0.067
r_chiral_restr	0.065
r_bond_other_d	0.037
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1776
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms

Software

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