8UN9 | pdb_00008un9

Crystal structure of the MrfB exonuclease catalytic core

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P50837	residues 33-279

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	The MrfB catalytic core (33-279) was crystallized by hanging drop with 1 microliter of 10 mg/mL protein (in 25 mM Tris pH 7.5, 125 mM NaCl, 1 mM TCEP, 5 mM MgCl2, 2 mM dTMP) and 1 microliter of well solution (0.1 M HEPES pH 7.5, 15% PEG Smear medium, 8% ethylene glycol). Crystals were harvested in 20 mM Tris pH 7.5, 125 mM NaCl, 1 mM TCEP, 5 mM MgCl2, 2 mM dTMP, 0.1 M HEPES pH 7.5, 20% PEG smear medium, and cryoprotected with the addition of 25% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.874	α = 90
b = 37.928	β = 99.147
c = 92.616	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	289	PIXEL	DECTRIS EIGER X 9M		2023-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.127129	APS	21-ID-D

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	2.1	45.72	99.6	0.064	0.076	0.04	0.998	14.2	6.5		29515

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	2.1	2.16	97.7		0.489	0.576	0.303	0.917	2.7	6.7

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.103	41.74	29500	1471	99.588	0.178	0.1749	0.1725	0.2325	0.2192	Random	51.814

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]
-0.623		0.36	2.184		-1.595

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.353
r_dihedral_angle_3_deg	14.997
r_lrange_it	7.96
r_lrange_other	7.919
r_dihedral_angle_1_deg	6.358
r_scangle_it	5.939
r_scangle_other	5.938
r_dihedral_angle_2_deg	5.572
r_mcangle_other	4.119
r_mcangle_it	4.117
r_scbond_it	3.855
r_scbond_other	3.854
r_mcbond_it	2.89
r_mcbond_other	2.889
r_angle_refined_deg	1.301
r_angle_other_deg	0.441
r_xyhbond_nbd_refined	0.263
r_nbd_refined	0.216
r_symmetry_nbd_other	0.194
r_nbd_other	0.185
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_other	0.176
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.128
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_metal_ion_refined	0.06
r_ncsr_local_group_1	0.055
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3766
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	2

Software

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