8QJQ | pdb_00008qjq

SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine - 5' - monophosphate as an inhibitor.

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	0.1 M Bis-Tris pH 5.5, 25 % w/v PEG 3350, 0.2 M Lithium sulfate, cryo-protection 25% v/v glycerol, protein concentration 7.5 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.255	α = 90
b = 73.166	β = 104.991
c = 81.66	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	1.8	41.78	99.4	0.108	0.117	0.995	14.2	6.7		45358			19.6

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	1.8	1.84	98.9		1.059	1.153	0.699	1.9	6.4

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	1.8	41.78	45328	2212	99.316	0.167	0.1675	0.1663	0.1787	0.2025	0.1808	Random	29.076

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]
1.031		-0.769	-1.087		0.409

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.218
r_dihedral_angle_4_deg	18.024
r_dihedral_angle_3_deg	13.754
r_dihedral_angle_other_3_deg	10.906
r_dihedral_angle_1_deg	6.613
r_lrange_it	6.477
r_lrange_other	6.241
r_scangle_it	4.053
r_scangle_other	3.932
r_mcangle_it	3.259
r_mcangle_other	3.258
r_scbond_it	2.674
r_scbond_other	2.469
r_mcbond_it	2.114
r_mcbond_other	2.113
r_angle_refined_deg	1.408
r_angle_other_deg	1.351
r_nbd_other	0.232
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.193
r_xyhbond_nbd_refined	0.187
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.155
r_symmetry_xyhbond_nbd_other	0.084
r_symmetry_nbtor_other	0.076
r_metal_ion_refined	0.072
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_ext_dist_refined_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3890
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	188

Software

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