Experiment: 9QGX

SciA(H42A) endonuclease from Escherichia phage T5 in complex with 10 bp DNA (GCGC sequence 1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	0.2 M sodium acetate trihydrate pH 7.0 and 20% (w/v) PEG 3350 (PEGIon screen condition G2, Hampton Research)

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.125	α = 90
b = 72.122	β = 96.627
c = 40.334	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	80	PIXEL	DECTRIS EIGER2 XE 16M		2023-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.347	36.06	99.6	0.206	0.988	6.2	6.7		7927			37.75

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	2.347	2.38	90		2.053	0.297	0.5	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.35	32.9	1.33	7827	417	98.6	0.2196	0.2169	0.2182	0.2665	0.2657	58.56

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	24.3648
f_angle_d	0.4836
f_chiral_restr	0.0371
f_plane_restr	0.0028
f_bond_d	0.0025

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	997
Nucleic Acid Atoms	404
Solvent Atoms	27
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing