8SAO | pdb_00008sao

Crystal structure of class III lanthipeptide synthetase ThurKC in complex with ThurA1 leader peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		282.15	15% glycerol, 16% PEG 6000, 80 mM sodium cacodylate pH 6.5, 160 mM calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.028	α = 90
b = 52.899	β = 95.728
c = 233.417	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		2019-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00385	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	2.5	232.3	96.9	0.093	0.104	0.995	9.8	4.5		66801

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	2.5	2.51			0.519	0.727

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	SAD	FREE R-VALUE	2.502	232.252	66800	3260	96.909	0.249	0.2456	0.25	0.3072	0.31	62.608

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]
-5.611		-0.241	2.175		3.415

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.244
r_dihedral_angle_3_deg	21.672
r_dihedral_angle_4_deg	21.545
r_lrange_it	10.271
r_dihedral_angle_1_deg	7.924
r_mcangle_it	6.465
r_scangle_it	6.107
r_mcbond_it	4.011
r_scbond_it	3.925
r_angle_refined_deg	1.242
r_nbtor_refined	0.316
r_ncsr_local_group_1	0.296
r_nbd_refined	0.254
r_symmetry_nbd_refined	0.248
r_xyhbond_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.184
r_ncsr_local_group_2	0.145
r_chiral_restr	0.114
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13859
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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