8SAM | pdb_00008sam

Crystal structure of class III lanthipeptide synthetase LP-GS-ThurKC in complex with ATP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		282.15	0.2 M potassium citrate tribasic monohydrate and 19 % w/v PEG 3350, protein incubated at 18 mg/mL with 3mM ATP and 3mM Magnesium Chloride and soaked for 6 hours with 7 mM ATP and 7 mM Calcium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.025	α = 90
b = 228.659	β = 100.504
c = 84.595	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		2021-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00798	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	2.15	49.005	86.6	0.091	0.103	0.998	9.1	4.1		94386

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	2.15	2.157	82.6		1.372	1.555	0.376	0.9	4.1

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	SAD	THROUGHOUT	2.15	49.005	94248	4665	86.441	0.205	0.203	0.21	0.2505	0.25	60.008

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]
-0.855		-0.701	3.844		-2.553

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.094
r_dihedral_angle_4_deg	19.509
r_dihedral_angle_3_deg	15.202
r_lrange_it	9.302
r_dihedral_angle_1_deg	6.808
r_scangle_it	6.668
r_mcangle_it	5.991
r_scbond_it	4.614
r_mcbond_it	3.969
r_angle_refined_deg	1.192
r_nbtor_refined	0.31
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.18
r_ncsr_local_group_1	0.131
r_chiral_restr	0.097
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13860
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	64

Software

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