- PDB-2c7k: Laue structure of phycoerythrocyanin from Mastigocladus laminosus -
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Open data
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Basic information
Entry
Database: PDB / ID: 2c7k
Title
Laue structure of phycoerythrocyanin from Mastigocladus laminosus
Components
PHYCOERYTHROCYANIN ALPHA CHAIN
PHYCOERYTHROCYANIN BETA CHAIN
Keywords
ELECTRON TRANSPORT / PHYCOERYTHROCYANIN / PHYCOVIOLOBILIN / PHYCOCYANOBILIN / BILE PIGMENT / CHROMOPHORE / PHOTOSYNTHESIS / PHYCOBILISOME / ANTENNA PROTEIN
Resolution: 3.2→50.3 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE CHROMOPHORES WHERE ATTACHED TO THE CYSTEINS USING RESTRAINTS FROM METHIONINE AND TREATED IN THE REFINEMENT AS REGULAR AMINO ACIDS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.286
208
2.2 %
RANDOM
Rwork
0.192
-
-
-
obs
0.192
5868
60.8 %
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Solvent computation
Bsol: 26.0488 Å2 / ksol: 0.152315 e/Å3
Displacement parameters
Biso mean: 38.4 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.465 Å2
-1.669 Å2
0 Å2
2-
-
3.465 Å2
0 Å2
3-
-
-
-6.929 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.33 Å
0.28 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.47 Å
0.55 Å
Refinement step
Cycle: LAST / Resolution: 3.2→50.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2534
0
129
186
2849
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.006507
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.24066
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
19.86
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
1.002
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
LS refinement shell
Resolution: 3.2→3.4 Å / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.274
-
0.5 %
Rwork
0.218
458
-
obs
-
-
33 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PROTEIN.PARAM
PROTEIN.TOP
X-RAY DIFFRACTION
2
WATER.PARAM
WATER.TOP
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