Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal grow
Temperature: 293 K Details: PROTEIN SOLUTION (10 MG/ML REDUCTIVELY METHYLATED PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0. ...Details: PROTEIN SOLUTION (10 MG/ML REDUCTIVELY METHYLATED PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0.3 M NaH2PO4, 1.7 M K2HPO4) AND CRYOPROTECTED WITH FOMBLIN FOLLOWED BY PARATONE N, vapor diffusion, hanging drop, temperature 293K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
Radiation
Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMETER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97929 Å / Relative weight: 1
Reflection
Resolution: 2.2→46.5 Å / Num. obs: 30718 / % possible obs: 96.1 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.469
Reflection shell
Resolution: 2.2→2.28 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.344 / % possible all: 73.4
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Phasing
Phasing
Method: MAD
Phasing MAD set
R cullis centric: 0 / Highest resolution: 2.2 Å / Lowest resolution: 41.87 Å / Power centric: 0
ID
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
0
0
26712
3870
ANO_1
0.688
1.558
25783
0
Phasing MAD set shell
R cullis centric: 0 / Power centric: 0
ID
Resolution (Å)
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
9.59-41.87
0
0
257
190
ISO_1
6.87-9.59
0
0
519
191
ISO_1
5.64-6.87
0
0
704
204
ISO_1
4.89-5.64
0
0
836
196
ISO_1
4.38-4.89
0
0
967
201
ISO_1
4-4.38
0
0
1061
194
ISO_1
3.71-4
0
0
1182
208
ISO_1
3.47-3.71
0
0
1266
197
ISO_1
3.27-3.47
0
0
1349
202
ISO_1
3.11-3.27
0
0
1428
189
ISO_1
2.96-3.11
0
0
1524
205
ISO_1
2.84-2.96
0
0
1592
205
ISO_1
2.73-2.84
0
0
1648
193
ISO_1
2.63-2.73
0
0
1747
205
ISO_1
2.54-2.63
0
0
1803
209
ISO_1
2.46-2.54
0
0
1851
192
ISO_1
2.39-2.46
0
0
1901
205
ISO_1
2.32-2.39
0
0
1847
186
ISO_1
2.26-2.32
0
0
1707
150
ISO_1
2.2-2.26
0
0
1523
148
ANO_1
9.59-41.87
0.467
2.492
257
0
ANO_1
6.87-9.59
0.431
2.825
519
0
ANO_1
5.64-6.87
0.388
3.354
704
0
ANO_1
4.89-5.64
0.431
3.04
836
0
ANO_1
4.38-4.89
0.506
2.666
966
0
ANO_1
4-4.38
0.516
2.655
1061
0
ANO_1
3.71-4
0.55
2.498
1181
0
ANO_1
3.47-3.71
0.531
2.45
1266
0
ANO_1
3.27-3.47
0.541
2.288
1349
0
ANO_1
3.11-3.27
0.587
1.991
1427
0
ANO_1
2.96-3.11
0.649
1.702
1524
0
ANO_1
2.84-2.96
0.739
1.384
1592
0
ANO_1
2.73-2.84
0.798
1.14
1648
0
ANO_1
2.63-2.73
0.85
0.949
1747
0
ANO_1
2.54-2.63
0.899
0.795
1796
0
ANO_1
2.46-2.54
0.937
0.638
1833
0
ANO_1
2.39-2.46
0.959
0.499
1834
0
ANO_1
2.32-2.39
0.971
0.437
1655
0
ANO_1
2.26-2.32
0.985
0.377
1417
0
ANO_1
2.2-2.26
0.987
0.257
1171
0
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
-4.058
-34.888
-150.982
SE
48.18
1.65
2
-6.415
-53.362
-125.385
SE
40.54
1.76
3
-6.761
-56.927
-71.288
SE
46.44
1.66
4
-3.854
-42.207
-0.331
SE
85.79
1.56
5
-9.42
-37.639
-151.781
SE
39.74
1.53
6
-1.226
-38.68
-135.828
SE
46.37
1.05
7
-7.011
-37.198
-0.156
SE
60.56
1.39
8
-1.071
-10.144
-128.34
SE
42.24
0.42
9
-4.072
-3.735
-102.235
SE
66.75
1.25
10
-5.609
-3.585
-76.774
SE
92.02
1.49
11
-17.428
-14.671
-32.925
SE
55.74
0.13
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 30581
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
9.21-100
72.8
0.617
503
7.25-9.21
66.7
0.868
505
6.19-7.25
61.6
0.834
565
5.5-6.19
60.8
0.858
640
4.99-5.5
57.4
0.888
714
4.61-4.99
62.4
0.93
748
4.3-4.61
56.9
0.924
829
4.04-4.3
61.5
0.901
878
3.83-4.04
60.5
0.905
920
3.64-3.83
61.8
0.892
968
3.49-3.64
62.1
0.884
1012
3.35-3.49
62.7
0.878
1034
3.22-3.35
63.1
0.856
1093
3.11-3.22
64.6
0.84
1099
3.01-3.11
66.1
0.836
1201
2.92-3.01
63.5
0.832
1174
2.83-2.92
67.5
0.8
1244
2.76-2.83
71
0.814
1241
2.69-2.76
69.3
0.79
1321
2.62-2.69
70.3
0.808
1309
2.56-2.62
73.7
0.798
1377
2.5-2.56
73.2
0.793
1370
2.45-2.5
78
0.787
1411
2.4-2.45
79
0.773
1464
2.35-2.4
79.7
0.785
1379
2.31-2.35
84.8
0.773
1400
2.27-2.31
83.7
0.752
1276
2.2-2.27
85
0.686
1906
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
DM
5
phasing
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datareduction
ARP/wARP
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 2.2→46.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.685 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.282
1546
5.044 %
RANDOM
Rwork
0.224
-
-
-
obs
0.227
30651
96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 25.85 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.786 Å2
0 Å2
0 Å2
2-
-
0.354 Å2
0 Å2
3-
-
-
-2.14 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→46.5 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3938
0
32
133
4103
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.02
0.022
4035
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.688
1.998
5473
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.758
5
503
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.179
24.689
177
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.586
15
717
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.782
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
635
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2992
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.232
0.2
1866
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.303
0.2
2715
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.168
0.2
224
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.105
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.168
0.2
31
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.27
0.2
2
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
0.861
1.5
2615
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.32
2
4064
X-RAY DIFFRACTION
r_scbond_it
2.291
3
1594
X-RAY DIFFRACTION
r_scangle_it
3.323
4.5
1407
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→2.25 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.354
83
-
Rwork
0.267
1566
-
obs
-
-
71.08 %
+
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