- PDB-3cbn: Crystal structure of a conserved protein (MTH639) from Methanobac... -
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Basic information
Entry
Database: PDB / ID: 3cbn
Title
Crystal structure of a conserved protein (MTH639) from Methanobacterium thermoautotrophicum
Components
Conserved protein MTH639Conservation
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / RP-A / 10241d / PSI-II / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
mth639 domain like / Protein of unknown function DUF371 / Mth639-like domain superfamily / Domain of unknown function (DUF371) / Jelly Rolls / Sandwich / Mainly Beta / Conserved protein
Function and homology information
Biological species
Methanothermobacter thermautotrophicus (archaea)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
Method to determine structure: SAD / Resolution: 1.63→29.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.244
574
-
RANDOM
Rwork
0.213
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-
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all
0.219
14179
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obs
0.213
14122
96.5 %
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Displacement parameters
Biso mean: 14.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.113 Å2
0 Å2
2.415 Å2
2-
-
-0.94 Å2
0 Å2
3-
-
-
1.052 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.25 Å
0.2 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.13 Å
0.11 Å
Refinement step
Cycle: LAST / Resolution: 1.63→29.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1136
0
0
126
1262
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
1.4
X-RAY DIFFRACTION
c_angle_deg
0.005
X-RAY DIFFRACTION
c_dihedral_angle_d
25.4
X-RAY DIFFRACTION
c_improper_angle_d
0.76
LS refinement shell
Resolution: 1.63→1.73 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.277
91
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Rwork
0.244
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-
obs
-
2153
92.5 %
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