8QJP

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with uridine - 5'- monophosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QJL	D_1292131829

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.1 M MES pH 6.5, 30 % w/v PEG 8000, 0.2 M Lithium sulfate. Protein concentration 11.8 mg/ml. Cryo-protection by glycerol 20 % v/v.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.434	α = 90
b = 72.8	β = 102.302
c = 82.928	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	100	PIXEL	DECTRIS PILATUS 2M		2022-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.2	43.41	97	0.081	0.09	0.998	11.5	5.1		155893			11.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	94		1.088	1.352	0.579	1.4	5.1

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	FREE R-VALUE	1.2	43.41	155884	7501	96.934	0.137	0.1369	0.1339	0.1669	random	20.454

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]
1.358		0.578	-1.124		-0.444

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.697
r_dihedral_angle_4_deg	18.558
r_dihedral_angle_3_deg	12.436
r_dihedral_angle_1_deg	6.121
r_lrange_it	3.82
r_lrange_other	3.442
r_scangle_other	3.274
r_scangle_it	3.267
r_rigid_bond_restr	3.105
r_scbond_it	2.835
r_scbond_other	2.822
r_mcangle_it	2.107
r_mcangle_other	2.099
r_mcbond_it	1.785
r_mcbond_other	1.776
r_angle_other_deg	1.573
r_angle_refined_deg	1.56
r_nbd_other	0.248
r_nbd_refined	0.228
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_other	0.131
r_symmetry_nbd_refined	0.12
r_chiral_restr	0.098
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.081
r_xyhbond_nbd_other	0.034
r_symmetry_metal_ion_refined	0.017
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3857
Nucleic Acid Atoms
Solvent Atoms	721
Heterogen Atoms	104

Software

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