9EMG | pdb_00009emg

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate as a product of c-di-GMP cleavage

X-RAY DIFFRACTION

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Starting Model(s)

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

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 5000. Protein concentration 7.5 mg/ml. Cryo-protection by glycerol 25 % v/v.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.34	α = 90
b = 72.637	β = 102.098
c = 82.94	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		2021-10-14	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	1.148	43.393	96.8	0.045	0.054	1	18.5	6.6		165597

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	1.148	1.182			0.567	0.701	0.824	2.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.148	43.393	165597	7969	90.609	0.113	0.1129	0.1107	0.1138	0.1311	0.1141	15.231

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]
0.218		0.075	-0.319		0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.984
r_dihedral_angle_4_deg	17.464
r_dihedral_angle_other_3_deg	15.08
r_dihedral_angle_3_deg	13.027
r_dihedral_angle_1_deg	5.936
r_lrange_it	3.589
r_lrange_other	2.768
r_scangle_it	2.679
r_scangle_other	2.654
r_rigid_bond_restr	2.237
r_scbond_it	2.228
r_scbond_other	2.218
r_mcangle_it	1.799
r_mcangle_other	1.799
r_angle_refined_deg	1.606
r_angle_other_deg	1.579
r_mcbond_it	1.44
r_mcbond_other	1.426
r_xyhbond_nbd_other	0.242
r_nbd_other	0.231
r_nbd_refined	0.23
r_symmetry_nbd_refined	0.221
r_symmetry_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.156
r_symmetry_metal_ion_refined	0.107
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.051
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3872
Nucleic Acid Atoms
Solvent Atoms	747
Heterogen Atoms	90

Software

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