Experiment: 8DCD

RNA ligase RtcB from Pyrococcus horikoshii in complex with Zn2+ and GTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ISZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 2 mM ZnCl2, 8 mM GTP, 20 % (w/v) sucrose

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.91	α = 90
b = 136.473	β = 90
c = 150.065	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2021-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.2822	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	2.22	49.27	99.6	0.039	0.998	15.7	14.2		82379			44.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.26	98.7		0.443	0.737	2	13.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ISZ	2.22	49.27	1.34	82303	4041	99.47	0.171	0.1697	0.1696	0.1971	0.1971	50.21

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.1372
f_angle_d	0.9543
f_chiral_restr	0.0566
f_plane_restr	0.0081
f_bond_d	0.0075

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7533
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	208

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing