7ESS

Structure-guided studies of the Holliday junction resolvase RuvX provide novel insights into ATP-stimulated cleavage of branched DNA and RNA substrates

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VHX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	300	0.1 M Bis-Tris propane, pH 7.0 and 2.4 M sodium malonate, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.49	α = 90
b = 42.58	β = 114.45
c = 58.11	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS		2021-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.93	53.477	99.3	0.067	0.075	0.034	13.2	4.7		19756

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	2.04	96.9		0.325	0.325	0.368	0.171	2.2	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VHX	1.93	52.95	18777	976	99.31	0.183	0.1809	0.2259	RANDOM	22.757

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]
-0.49		-0.53	0.78		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	20.444
r_dihedral_angle_2_deg	17.967
r_dihedral_angle_3_deg	15.594
r_dihedral_angle_1_deg	5.437
r_angle_other_deg	3.631
r_angle_refined_deg	1.484
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	20.444
r_dihedral_angle_2_deg	17.967
r_dihedral_angle_3_deg	15.594
r_dihedral_angle_1_deg	5.437
r_angle_other_deg	3.631
r_angle_refined_deg	1.484
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2208
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.