6YQ3

Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis

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		291	20% PEG 3350, 0.1 M Na Malonate, 0.1 M BIS-TRIS prop, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.969	α = 90
b = 60.214	β = 102.458
c = 88.308	γ = 90

Symmetry
Space Group	I 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	298	CCD	ADSC QUANTUM 315		2019-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.57	24.7	98.1	0.053	0.064	0.999	22.5	2.9		60525			16.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.61			0.464	0.566	0.818	2.7	2.8

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	FREE R-VALUE	4osp	1.57	24.696	60524	3027	96.07	0.143	0.1421	0.15	0.1663	0.18	16.537

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]
-0.832		-0.522	1.231		-0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.991
r_dihedral_angle_4_deg	17.051
r_dihedral_angle_3_deg	11.637
r_dihedral_angle_1_deg	6.293
r_lrange_it	5.555
r_lrange_other	5.432
r_scangle_it	3.823
r_scangle_other	3.822
r_scbond_it	2.448
r_scbond_other	2.447
r_angle_refined_deg	2.114
r_mcangle_it	1.958
r_mcangle_other	1.953
r_angle_other_deg	1.681
r_chiral_restr_other	1.651
r_mcbond_it	1.291
r_mcbond_other	1.287
r_nbd_other	0.237
r_nbd_refined	0.229
r_symmetry_nbd_refined	0.203
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.075
r_symmetry_xyhbond_nbd_other	0.068
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3733
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	156

Software

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