8QJM | pdb_00008qjm

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	0.2 M Lithium sulfate 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350. Protein concentration 7.5 mg/ml. Cryo-protection by PEG400 30 % v/v.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.139	α = 90
b = 72.805	β = 105.066
c = 81.238	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	Bruker PHOTON II	HELIOS MX, Ga	2019-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2 70 kV	1.3418

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	41.66	99.2	0.124	0.149	0.961	6.8	3.2		57878

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			0.596	0.722	0.559

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	1.65	41.66	57816	2819	99.012	0.173	0.1732	0.1726	0.1856	0.1979	0.1861	Random	12.199

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]
1.178		-0.898	-0.499		-0.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.632
r_dihedral_angle_4_deg	18.296
r_dihedral_angle_3_deg	15.632
r_dihedral_angle_1_deg	6.379
r_lrange_it	4.912
r_lrange_other	4.547
r_scangle_other	2.755
r_scangle_it	2.75
r_scbond_it	1.734
r_scbond_other	1.706
r_mcangle_other	1.661
r_mcangle_it	1.66
r_angle_refined_deg	1.607
r_angle_other_deg	1.474
r_mcbond_it	1.068
r_mcbond_other	1.064
r_nbd_other	0.234
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.08
r_metal_ion_refined	0.066
r_symmetry_metal_ion_refined	0.052
r_symmetry_xyhbond_nbd_other	0.037
r_xyhbond_nbd_other	0.022
r_bond_refined_d	0.011
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	3880
Nucleic Acid Atoms
Solvent Atoms	538
Heterogen Atoms	151

Software

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