Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 17.6% PEG 2000, 0.047 M MgCl2, 5% glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
93
1
2
100
1
3
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
ROTATING ANODE
1
1.5419
SYNCHROTRON
APS
19-ID
2
1.0083
SYNCHROTRON
APS
5ID-B
3
1.1405
Detector
Type
ID
Detector
Date
RIGAKU RAXIS IV++
1
IMAGE PLATE
May 14, 2006
2
CCD
May 14, 2006
3
CCD
May 14, 2006
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
NiFilter
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
3
SINGLEWAVELENGTH
M
x-ray
3
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.5419
1
2
1.0083
1
3
1.1405
1
Reflection
Redundancy: 5.4 % / Av σ(I) over netI: 7.8 / Number: 224137 / Rmerge(I) obs: 0.085 / Χ2: 1.6 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 41854 / % possible obs: 94.1
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
4.2
50
99.9
1
0.049
1.84
6.2
3.33
4.2
100
1
0.068
1.945
6.4
2.91
3.33
100
1
0.078
1.078
6.2
2.65
2.91
99.8
1
0.126
1.256
6
2.46
2.65
99.8
1
0.17
0.948
5.8
2.31
2.46
99.3
1
0.225
0.875
5.6
2.2
2.31
99
1
0.323
1.979
5.3
2.1
2.2
97
1
0.408
0.884
4.6
2.02
2.1
85.7
1
0.571
5.948
3.5
1.95
2.02
59.9
1
0.528
0.797
2.4
Reflection
Resolution: 1.91→50 Å / Num. obs: 46776 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Χ2: 2.306 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.91-1.98
6.7
0.532
4630
1.534
98.4
1.98-2.06
6.9
0.373
4523
1.688
97.4
2.06-2.15
7
0.289
4547
1.856
97.2
2.15-2.26
7.1
0.217
4591
2.064
97.2
2.26-2.41
7.2
0.169
4615
2.225
98.7
2.41-2.59
7.5
0.135
4686
2.244
99.6
2.59-2.85
7.9
0.101
4719
2.373
99.9
2.85-3.27
8.4
0.075
4752
2.563
100
3.27-4.11
8.6
0.051
4769
2.857
100
4.11-50
8.3
0.042
4944
3.1
99.7
-
Phasing
Phasing
Method: MIRAS
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 46739
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
8.99-100
25.9
0.871
501
6.78-8.99
19
0.928
638
5.67-6.78
26.3
0.906
782
4.97-5.67
21.2
0.914
896
4.48-4.97
18.5
0.924
1018
4.11-4.48
15.2
0.938
1097
3.82-4.11
15.7
0.92
1186
3.58-3.82
14.4
0.932
1269
3.39-3.58
16.7
0.923
1335
3.22-3.39
19.7
0.901
1410
3.07-3.22
24.4
0.883
1484
2.94-3.07
56.6
0.809
1529
2.83-2.94
92.7
0.736
1588
2.73-2.83
90.6
0.703
1652
2.64-2.73
91
0.733
1713
2.56-2.64
89
0.716
1781
2.48-2.56
89.6
0.739
1823
2.41-2.48
92.3
0.681
1858
2.35-2.41
90.9
0.705
1890
2.29-2.35
90.5
0.704
1974
2.24-2.29
90.1
0.735
1946
2.19-2.24
88.1
0.698
2016
2.14-2.19
89.2
0.733
2068
2.1-2.14
91.1
0.714
2075
2.05-2.1
91.4
0.722
2150
2.01-2.05
88.6
0.679
2181
1.98-2.01
90.4
0.682
2211
1.94-1.98
90.1
0.638
2307
1.91-1.94
91.4
0.621
2361
Phasing MIR der
ID
Der set-ID
1
1
2
1
Phasing MIR der site
ID
Der-ID
Biso (Å)
Atom type symbol
Fract x
Fract y
Fract z
Occupancy
1
1
35.4654
Hg
0.8871
0.2179
0.1109
0.2056
1
2
60
Hg
0.501
0.058
0.0756
0.0593
2
1
60
Os
0.6627
0.1792
0.0325
0.3294
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
2.05
phasing
DM
4.2
phasing
REFMAC
refinement
PDB_EXTRACT
3.004
dataextraction
Refinement
Method to determine structure: MIRAS / Resolution: 1.91→30.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.004 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.216
2371
5.1 %
RANDOM
Rwork
0.159
-
-
-
obs
0.162
46738
98.65 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.049 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1 Å2
0 Å2
0 Å2
2-
-
-0.06 Å2
0 Å2
3-
-
-
-0.04 Å2
Refinement step
Cycle: LAST / Resolution: 1.91→30.69 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4225
0
76
441
4742
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
4381
X-RAY DIFFRACTION
r_angle_refined_deg
1.353
1.983
5912
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.034
5
552
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.3
24.413
179
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.295
15
760
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.36
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.113
0.2
660
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
3238
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.2
2152
X-RAY DIFFRACTION
r_nbtor_refined
0.309
0.2
3065
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.155
0.2
362
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.214
0.2
103
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.168
0.2
40
X-RAY DIFFRACTION
r_mcbond_it
3.728
1.5
2822
X-RAY DIFFRACTION
r_mcangle_it
4.221
2
4371
X-RAY DIFFRACTION
r_scbond_it
7.019
3
1806
X-RAY DIFFRACTION
r_scangle_it
9.717
4.5
1541
LS refinement shell
Resolution: 1.91→1.957 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.371
165
-
Rwork
0.234
3122
-
all
-
3287
-
obs
-
-
95.83 %
+
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