8S4T

DNA bound structure of PrgE from plasmid pCF10

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		293	15 % Polyethylene glycol 400, 50 mM MES pH 6.5, 80 mM Magnesium acetate, 15 mM Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.776	α = 90
b = 90.043	β = 90
c = 131.848	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		2023-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.67	49.74	99.75	0.1158	0.998	10.71	6.7		26266			73.16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.765	99.06		2.067	0.628	0.95	7

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.67	49.74	24963	1275	99.81	0.231	0.23052	0.22939	0.25257	RANDOM	94.065

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]
-0.54			1.24		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.975
r_dihedral_angle_1_deg	6.258
r_long_range_B_refined	5.063
r_long_range_B_other	5.063
r_dihedral_angle_2_deg	3.091
r_mcangle_it	2.731
r_mcangle_other	2.731
r_scangle_other	2.586
r_mcbond_it	1.532
r_mcbond_other	1.532
r_scbond_it	1.405
r_scbond_other	1.404
r_angle_refined_deg	0.683
r_angle_other_deg	0.254
r_chiral_restr	0.035
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms	315
Solvent Atoms	9
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building