8YND

ATP-grasp peptide ligase from Streptomyces

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL18U1
Synchrotron site	SSRF
Beamline	BL18U1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-09-10
Detector	STFC Large Pixel Detector
Wavelength(s)	0.97915
Spacegroup name	P 1
Unit cell lengths	87.928, 100.641, 131.555
Unit cell angles	99.54, 101.88, 115.94

Refinement procedure

Resolution	50.000 - 2.190
R-factor	0.2139
Rwork	0.211
R-free	0.26280
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.008
RMSD bond angle	1.055
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX ((1.19.2_4158: ???))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.240
High resolution limit [Å]	2.190	5.970	2.200
Rmerge	0.104	0.034	0.734
Rmeas	0.123	0.041	0.873
Rpim	0.065	0.022	0.466
Number of reflections	188982	9571	9439
<I/σ(I)>	5.9
Completeness [%]	98.3	99.6	97.4
Redundancy	3.5	3.2	3.4
CC(1/2)	0.982	0.991	0.603

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293.15	MgCl2.6H2O, Trisodium citrate dihydrate, Bis-Tris-Propane PH7.5, PEG Smear High