Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
-
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: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 10mM Tris pH8.5 and 200mM sodium nitrate. The crystals were transfered to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid ...Details: 1-1.3M ammonium sulfate, 6-8% dioxane, 60-80mM MES pH 6.5, 10mM Tris pH8.5 and 200mM sodium nitrate. The crystals were transfered to 2.1M NaMalonate (pH 7.0) prior to freezing in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ALS
5.0.2
1
0.9804
SYNCHROTRON
ALS
5.0.2
2
1
Detector
Type
ID
Detector
Date
ADSC QUANTUM 315
1
CCD
Sep 29, 2006
ADSC QUANTUM 315
2
CCD
Sep 29, 2006
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SAD
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9804
1
2
1
1
Reflection
Resolution: 2.8→50 Å / Num. obs: 39158 / % possible obs: 84.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
2.8-2.9
2.4
0.319
36
2.9-3.02
2.6
0.287
54.2
3.02-3.15
2.8
0.264
79.8
3.15-3.32
3.3
0.215
96.7
3.32-3.53
3.6
0.157
98.8
3.53-3.8
3.6
0.108
98.1
3.8-4.18
3.6
0.076
97.8
4.18-4.79
3.5
0.058
96.8
4.79-6.03
3.3
0.051
95.8
6.03-50
3.5
0.037
93.1
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
BUSTER-TNT
BUSTER2.9.2
refinement
PDB_EXTRACT
3.1
dataextraction
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SHARP
phasing
BUSTER
2.9.2
refinement
Refinement
Resolution: 2.8→27.12 Å / Cor.coef. Fo:Fc: 0.8959 / Cor.coef. Fo:Fc free: 0.8721 / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2408
1845
4.96 %
RANDOM
Rwork
0.2138
-
-
-
obs
0.2151
37201
-
-
Displacement parameters
Biso mean: 97.39 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-15.5692 Å2
0 Å2
0 Å2
2-
-
-15.5692 Å2
0 Å2
3-
-
-
31.1385 Å2
Refine analyze
Luzzati coordinate error obs: 0.532 Å
Refinement step
Cycle: LAST / Resolution: 2.8→27.12 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5324
0
80
53
5457
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
5654
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.06
7758
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1772
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
132
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
871
HARMONIC
5
X-RAY DIFFRACTION
t_it
5654
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.44
X-RAY DIFFRACTION
t_other_torsion
21.29
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
724
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
6
HARMONIC
1
X-RAY DIFFRACTION
t_utility_distance
20
HARMONIC
1
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
6195
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.87 Å / Total num. of bins used: 19
Rfactor
Num. reflection
% reflection
Rfree
0.3524
48
4.75 %
Rwork
0.2832
962
-
all
0.2864
1010
-
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.6612
-1.6642
2.0276
0.56
-2.1814
5.6756
0.001
-0.5805
-0.0558
0.2539
0.0899
-0.2256
-0.2206
0.1078
-0.0909
-0.2245
-0.0422
-0.1209
0.1687
0.0039
-0.1986
62.1708
45.9357
36.8736
2
5.2767
-0.9099
-2.091
3.2685
2.1534
6.2873
0.032
-0.6011
0.281
0.2819
0.0827
0.1838
0.0056
-0.1084
-0.1147
-0.3007
-0.0676
0.0067
0.1283
-0.0157
-0.2726
37.8551
56.9652
36.0082
3
-2.176
1.6252
-1.6568
2.6687
2.1399
1.1743
0.0763
-0.216
0.101
0.0873
-0.0185
-0.097
-0.1785
-0.0796
-0.0578
-0.1034
-0.2417
0.0937
0.1397
-0.1214
-0.1565
21.6673
78.0336
65.4585
4
4.3164
-1.199
-0.2973
2.0217
0.2375
3.4957
0.1822
-0.0641
-0.0738
-0.2127
0.0716
-0.1937
0.208
0.5965
-0.2538
-0.2767
-0.0485
-0.0664
0.1183
-0.0253
-0.1948
63.0695
46.92
19.4082
5
3.8769
-0.0624
0.3342
3.9242
0.4331
5.3816
0.1698
0.1744
-0.217
-0.5185
-0.0844
-0.2045
-0.0412
0.5619
-0.0854
-0.0648
0.2336
0.0824
0.0164
-0.1108
-0.2963
62.5751
44.7246
-19.914
6
3.1537
0.9955
0.0658
2.8985
3.3734
3.1946
0.0101
0.0769
0.3221
-0.0013
-0.0772
-0.0933
-0.3593
0.0192
0.0671
-0.1769
-0.2456
0.1125
0.1716
-0.1105
-0.0212
32.5675
79.2559
51.4906
7
3.8759
0.9153
-1.0364
2.1049
-0.1892
6.1248
0.145
0.3438
-0.1027
-0.2331
-0.1185
-0.2343
-0.3006
0.3627
-0.0265
-0.1306
0.0334
-0.0174
-0.0781
-0.035
-0.2262
55.2822
52.5889
-4.3181
8
4.501
-1.3576
-0.2251
0.3731
-0.0605
2.3128
0.363
-0.1304
0.087
-0.2296
-0.0139
-0.0091
-0.1533
-0.4593
-0.3491
-0.2135
-0.0535
-0.0376
0.0441
0.0117
-0.1397
37.1227
53.8072
18.885
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{ A29-A128 }
A
29 - 128
2
X-RAY DIFFRACTION
2
{ B31-B129 }
B
31 - 129
3
X-RAY DIFFRACTION
3
{ C35-C57 C66-C75 C|81-C91 C101-C124 }
C
35 - 57
4
X-RAY DIFFRACTION
3
{ C35-C57 C66-C75 C|81-C91 C101-C124 }
C
66 - 75
5
X-RAY DIFFRACTION
3
{ C35-C57 C66-C75 C|81-C91 C101-C124 }
C
81 - 91
6
X-RAY DIFFRACTION
3
{ C35-C57 C66-C75 C|81-C91 C101-C124 }
C
101 - 124
7
X-RAY DIFFRACTION
4
{ D27-D116 }
D
27 - 116
8
X-RAY DIFFRACTION
5
{ E27-E105 }
E
27 - 105
9
X-RAY DIFFRACTION
6
{ F27-F105 }
F
27 - 105
10
X-RAY DIFFRACTION
7
{ J32-J128 }
J
32 - 128
11
X-RAY DIFFRACTION
8
{ R27-R117 }
R
27 - 117
+
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