endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Resolution: 2.1→2.2 Å / Redundancy: 9.17 % / Rmerge(I) obs: 0.0682 / Mean I/σ(I) obs: 13.36 / Num. unique all: 1104 / % possible all: 100
-
Phasing
Phasing MR
Cor.coef. Fo:Fc: 0.73 / Packing: 0.542
Highest resolution
Lowest resolution
Method
Reflection percent
σ(F)
Translation
3 Å
15 Å
general
99.9
0
-
Processing
Software
Name
Version
Classification
NB
CNS
refinement
PDB_EXTRACT
2
dataextraction
APEX
datacollection
APEX
datareduction
CNS
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Staphylococcal nuclease V66E/P117G/H124L/S128A variant with b-factors set to 20.0 A^2 and residue 66 truncated to Ala; waters removed Resolution: 2.1→50 Å / σ(F): 0 / σ(I): 0
Rfactor
Num. reflection
% reflection
Rfree
0.265
897
10.6 %
Rwork
0.211
-
-
all
0.218
8478
-
obs
0.208
8460
99.8 %
Solvent computation
Bsol: 55.494 Å2
Displacement parameters
Biso mean: 24.433 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.634 Å2
0 Å2
0 Å2
2-
-
-0.634 Å2
0 Å2
3-
-
-
1.268 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1038
0
5
74
1117
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_mcbond_it
1.356
1.5
X-RAY DIFFRACTION
c_scbond_it
2.331
2
X-RAY DIFFRACTION
c_mcangle_it
2.073
2
X-RAY DIFFRACTION
c_scangle_it
3.358
2.5
LS refinement shell
Resolution: 2.1→2.14 Å
Rfactor
Num. reflection
% reflection
Rfree
0.332
49
-
Rwork
0.237
-
-
obs
-
486
99.9 %
Xplor file
Refine-ID
Serial no
Param file
X-RAY DIFFRACTION
1
CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION
2
CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION
3
CNS_TOPPAR:ion.param
+
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