8QJN

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with adenosine-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	0.2 M Ammonium sulfate 0.1 M MES pH 6.5, 30% w/v Polyethylene glycol 8000. Protein concentration 8.5 mg/ml. Cryo-protection by glycerol 20 % v/v.

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.47	α = 90
b = 72.741	β = 102.684
c = 82.752	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 6M		2021-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.65	43.385	88.8	0.105	0.113	0.998	13.2	6.9		52701

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	1.65	1.69	92.8		0.869	0.935	0.777	2.2

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	1.65	43.385	52701	2536	85.069	0.176	0.1759	0.1747	0.2143	Random	19.032

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]
0.156		0.37	-0.33		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.664
r_dihedral_angle_4_deg	21.353
r_dihedral_angle_3_deg	14.055
r_dihedral_angle_1_deg	6.339
r_lrange_it	6.143
r_lrange_other	5.816
r_scangle_it	3.895
r_scangle_other	3.862
r_mcangle_it	2.561
r_mcangle_other	2.555
r_scbond_it	2.535
r_scbond_other	2.461
r_mcbond_it	1.631
r_mcbond_other	1.622
r_angle_refined_deg	1.569
r_angle_other_deg	1.469
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.203
r_nbd_other	0.184
r_symmetry_nbd_other	0.181
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.144
r_chiral_restr	0.086
r_metal_ion_refined	0.081
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3809
Nucleic Acid Atoms
Solvent Atoms	589
Heterogen Atoms	55

Software

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