8Q5O

N-terminal domain of restriction endonuclease Eco15I with tetra-methylated target DNA.

X-RAY DIFFRACTION

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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	6.5	291	0.1 M HEPES, pH 6.5, 0.02 M CaCl2, 35 % pentaerythritol ethoxylate

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.995	α = 90
b = 95.995	β = 90
c = 96.307	γ = 120

Symmetry
Space Group	P 32 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	PIXEL	DECTRIS PILATUS 6M		2020-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.33	47.998	99.77	0.1096	0.1127	0.02591	0.999	20.04	19.6		22349			51.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.413	99.68		1.294	1.327	0.2899	0.961	4.33	20.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.33	47.998	22347	1249	99.902	0.265	0.2641	0.276	127.653

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]
17.783			17.783		-35.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.878
r_dihedral_angle_6_deg	15.012
r_dihedral_angle_2_deg	12.881
r_lrange_it	12.449
r_lrange_other	12.447
r_mcangle_it	9.179
r_mcangle_other	9.176
r_scangle_it	8.186
r_scangle_other	8.184
r_mcbond_it	6.397
r_mcbond_other	6.232
r_scbond_it	5.546
r_scbond_other	5.545
r_dihedral_angle_1_deg	4.998
r_angle_refined_deg	1.3
r_dihedral_angle_other_2_deg	0.885
r_angle_other_deg	0.672
r_symmetry_nbd_refined	0.669
r_nbd_other	0.385
r_symmetry_xyhbond_nbd_refined	0.355
r_symmetry_nbd_other	0.267
r_metal_ion_refined	0.252
r_ncsr_local_group_1	0.252
r_nbd_refined	0.224
r_nbtor_refined	0.201
r_xyhbond_nbd_refined	0.191
r_xyhbond_nbd_other	0.143
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.059
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2293
Nucleic Acid Atoms	367
Solvent Atoms	24
Heterogen Atoms	2

Software

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