- PDB-2e4l: Thermodynamic and Structural Analysis of Thermolabile RNase HI fr... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2e4l
Title
Thermodynamic and Structural Analysis of Thermolabile RNase HI from Shewanella oneidensis MR-1
Components
Ribonuclease HI
Keywords
HYDROLASE / endoribonuclease / RNase HI / Shewanella oneidensis MR-1
Function / homology
Function and homology information
DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function
Ribonuclease HI / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2→27.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.12 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21851
801
4.9 %
RANDOM
Rwork
0.18871
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-
-
obs
0.19017
15432
99.95 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 23.202 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2→27.22 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1223
0
0
163
1386
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.035
0.021
1252
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1111
X-RAY DIFFRACTION
r_angle_refined_deg
2.314
1.928
1692
X-RAY DIFFRACTION
r_angle_other_deg
1.015
3
2597
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.136
3
154
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.164
15
229
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.29
0.2
179
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
1389
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
244
X-RAY DIFFRACTION
r_nbd_refined
0.256
0.3
282
X-RAY DIFFRACTION
r_nbd_other
0.249
0.3
1064
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.237
0.5
123
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.453
0.3
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.141
0.3
20
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.544
0.5
19
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.728
1.5
767
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.949
2
1226
X-RAY DIFFRACTION
r_scbond_it
4.401
3
485
X-RAY DIFFRACTION
r_scangle_it
6.728
4.5
466
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20 /
Rfactor
Num. reflection
Rfree
0.259
56
Rwork
0.196
1133
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
protein_rep.param
protein.top
X-RAY DIFFRACTION
2
water_rep.param
water.top
X-RAY DIFFRACTION
3
ion.param
ion.top
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