8SAP | pdb_00008sap

Crystal structure of class III lanthipeptide synthetase ThurKC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SAM	model used for molecular replacement was obtained in the same body of work

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		282.15	18% (w/v) PEG 3350, 100 mM Bis tris propane/ hydrochloric acid pH 7.5, 200 mM sodium fluoride, and 3% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.296	α = 90
b = 230.23	β = 100.617
c = 84.383	γ = 90

Symmetry
Space Group	P 1 21 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 9M		2020-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12706	APS	21-ID-D

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	2.52	115.115	98.9	0.067	0.075	0.998	12.4	4.7		68899

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	2.52	2.528			0.824	0.829	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.52	115.115	68899	3422	98.889	0.192	0.1892	0.19	0.2503	0.25	87.984

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]
3.056		-1.312	3.1		-5.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.94
r_dihedral_angle_4_deg	20.298
r_dihedral_angle_3_deg	17.603
r_lrange_it	14.335
r_scangle_it	9.95
r_mcangle_it	9.332
r_dihedral_angle_1_deg	7.092
r_scbond_it	6.66
r_mcbond_it	6.131
r_angle_refined_deg	1.239
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.202
r_ncsr_local_group_1	0.148
r_symmetry_xyhbond_nbd_refined	0.124
r_chiral_restr	0.109
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13522
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
CRANK2	phasing