- PDB-4ar5: X-ray crystallographic structure of the oxidised form perdeuterat... -
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Basic information
Entry
Database: PDB / ID: 4ar5
Title
X-ray crystallographic structure of the oxidised form perdeuterated Pyrococcus furiosus rubredoxin in D2O at 295K (in quartz capillary) to 1.00 Angstrom resolution.
Components
RUBREDOXIN
Keywords
ELECTRON TRANSPORT / PERDEUTERATED / AMBIENT CAPILLARY
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.77 Å / Relative weight: 1
Reflection
Resolution: 1→35.32 Å / Num. obs: 28427 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 11.15 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.4
Reflection shell
Resolution: 1→1.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 98
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
PHENIX
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS Starting model: 100 K 0.80 A RESOLUTION OXIDISED PF RUBREDOXIN STRUCTURE. Resolution: 1→27.54 Å / SU ML: 0.06 / σ(F): 1.36 / Phase error: 8.98 / Stereochemistry target values: ML Details: CRYSTAL SEALED IN A QUARTZ CAPILLARY FOR 295K X-RAY DATA COLLECTION ON 2 DIFFERENT ZONES OVER TOTAL 90 DEGREES OSCILLATION ROTATION.
Rfactor
Num. reflection
% reflection
Rfree
0.1189
1439
5.1 %
Rwork
0.1095
-
-
obs
0.1099
28386
95.92 %
Solvent computation
Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 104.285 Å2 / ksol: 0.5 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
0.2004 Å2
0 Å2
0 Å2
2-
-
-0.1398 Å2
0 Å2
3-
-
-
-0.0606 Å2
Refinement step
Cycle: LAST / Resolution: 1→27.54 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
421
0
1
135
557
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
479
X-RAY DIFFRACTION
f_angle_d
1.229
657
X-RAY DIFFRACTION
f_dihedral_angle_d
11.701
186
X-RAY DIFFRACTION
f_chiral_restr
0.079
64
X-RAY DIFFRACTION
f_plane_restr
0.008
90
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1-1.0357
0.2243
154
0.2001
2689
X-RAY DIFFRACTION
98
1.0357-1.0772
0.1519
142
0.1596
2629
X-RAY DIFFRACTION
95
1.0772-1.1262
0.1135
143
0.1131
2736
X-RAY DIFFRACTION
99
1.1262-1.1856
0.1103
160
0.0963
2766
X-RAY DIFFRACTION
99
1.1856-1.2599
0.1086
149
0.0926
2710
X-RAY DIFFRACTION
98
1.2599-1.3572
0.1006
137
0.0892
2651
X-RAY DIFFRACTION
95
1.3572-1.4938
0.098
131
0.0821
2727
X-RAY DIFFRACTION
96
1.4938-1.7099
0.1009
142
0.079
2707
X-RAY DIFFRACTION
96
1.7099-2.1541
0.1122
142
0.0912
2661
X-RAY DIFFRACTION
93
2.1541-27.5504
0.127
139
0.1296
2671
X-RAY DIFFRACTION
89
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