8QJO | pdb_00008qjo

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-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	5.5	291	0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, protein concentration 7.5 mg/ml. Cryo-protection by glycerol 20 % v/v.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.178	α = 90
b = 73.068	β = 105.324
c = 81.607	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		2020-11-20	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	1.85	41.64	96.4	0.129	0.152	0.994	7.1	3.5		40335			19.2

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	1.85	1.89	99.3		1.295	1.523	0.376	1.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.85	41.64	40318	2029	96.312	0.172	0.1723	0.1714	0.1805	0.2091	0.1845	Random	27.984

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]
1.471		0.222	-1.479		-0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.346
r_dihedral_angle_4_deg	17.843
r_dihedral_angle_3_deg	14.532
r_dihedral_angle_1_deg	6.625
r_lrange_it	6.254
r_lrange_other	6.155
r_scangle_it	4.41
r_scangle_other	4.343
r_mcangle_it	3.276
r_mcangle_other	3.276
r_scbond_it	2.809
r_scbond_other	2.686
r_mcbond_it	2.099
r_mcbond_other	2.099
r_angle_refined_deg	1.445
r_angle_other_deg	1.339
r_symmetry_nbd_refined	0.232
r_nbd_other	0.228
r_nbd_refined	0.215
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_metal_ion_refined	0.075
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	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	3842
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	197

Software

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