- PDB-4ar6: X-ray crystallographic structure of the reduced form perdeuterate... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4ar6
Title
X-ray crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin at 295 K (in quartz capillary) to 0.92 Angstroms resolution.
Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: D2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.46 Å3/Da / Density % sol: 14.97 % Description: SOLVED BY RIGID BODY FIT FROM 100 K 0.75 A RESOLUTION REDUCED PF RUBREDOXIN STRUCTURE.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.77 Å / Relative weight: 1
Reflection
Resolution: 0.92→43.94 Å / Num. obs: 37464 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.06 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.4
Reflection shell
Resolution: 0.92→0.97 Å / Redundancy: 4.22 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 94.8
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
PHENIX
phasing
Refinement
Method to determine structure: OTHER / Resolution: 0.92→27.465 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 9.92 / Stereochemistry target values: ML Details: CRYSTAL WAS REDUCED WITH SODIUM DITHIONITE IN D2O AND THEN SEALED IN A QUARTZ CAPILLARY FOR 295 K DATA COLLECTION. 8 DIFFERENT ZONES OF THE SAME CRYSTAL (VOLUME 0.012 MM3) WERE EXPOSED TO X- ...Details: CRYSTAL WAS REDUCED WITH SODIUM DITHIONITE IN D2O AND THEN SEALED IN A QUARTZ CAPILLARY FOR 295 K DATA COLLECTION. 8 DIFFERENT ZONES OF THE SAME CRYSTAL (VOLUME 0.012 MM3) WERE EXPOSED TO X-RAYS OVER 180 DEGREES OSCILLATION ROTATION. DATA WAS SCALED AND MERGED.
Rfactor
Num. reflection
% reflection
Rfree
0.1361
1864
5 %
Rwork
0.1285
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obs
0.1288
37395
99.18 %
Solvent computation
Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 121.734 Å2 / ksol: 0.591 e/Å3
Displacement parameters
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: 0.92→27.465 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
421
0
1
143
565
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
479
X-RAY DIFFRACTION
f_angle_d
1.247
657
X-RAY DIFFRACTION
f_dihedral_angle_d
11.275
186
X-RAY DIFFRACTION
f_chiral_restr
0.085
64
X-RAY DIFFRACTION
f_plane_restr
0.007
90
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
0.92-0.9449
0.2561
127
0.23
2509
X-RAY DIFFRACTION
92
0.9449-0.9727
0.1804
132
0.1709
2648
X-RAY DIFFRACTION
98
0.9727-1.0041
0.1462
137
0.1237
2748
X-RAY DIFFRACTION
100
1.0041-1.04
0.1172
129
0.1047
2710
X-RAY DIFFRACTION
100
1.04-1.0816
0.106
150
0.092
2714
X-RAY DIFFRACTION
100
1.0816-1.1308
0.091
137
0.0842
2717
X-RAY DIFFRACTION
100
1.1308-1.1905
0.1003
134
0.0825
2753
X-RAY DIFFRACTION
100
1.1905-1.265
0.1012
160
0.0892
2730
X-RAY DIFFRACTION
100
1.265-1.3627
0.1154
124
0.0951
2771
X-RAY DIFFRACTION
100
1.3627-1.4998
0.1028
163
0.1012
2739
X-RAY DIFFRACTION
100
1.4998-1.7169
0.1241
149
0.1081
2765
X-RAY DIFFRACTION
100
1.7169-2.1629
0.1318
166
0.1244
2797
X-RAY DIFFRACTION
100
2.1629-27.477
0.1619
156
0.1569
2930
X-RAY DIFFRACTION
100
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