Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 4.65 Å3/Da / Density % sol: 73.55 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 - 25% PEG 350 MME, 0.1 M MES, pH 6.5, 250-450 mM CaCl2, 5% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: NSLS / Beamline: X29A
Detector
Type: ADSC QUANTUM 315 / Detector: CCD
Radiation
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 4.65→89 Å / Num. all: 51604 / Num. obs: 37155 / % possible obs: 72 %
-
Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
PHASER
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.66→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 363.659 / SU ML: 1.8 / Cross valid method: THROUGHOUT / ESU R Free: 1.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29374
997
5.3 %
RANDOM
Rwork
0.25526
-
-
-
obs
0.25731
17755
73.12 %
-
all
-
24282
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 283.463 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.04 Å2
0 Å2
3.65 Å2
2-
-
-2.77 Å2
0 Å2
3-
-
-
6.76 Å2
Refinement step
Cycle: LAST / Resolution: 4.66→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
17972
0
66
0
18038
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
18367
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.135
1.985
25036
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.866
5
2411
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
27.294
23.691
550
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.762
15
3000
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.059
15
48
X-RAY DIFFRACTION
r_chiral_restr
0.071
0.2
3160
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
13118
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
0.263
1.5
11995
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.545
2
19351
X-RAY DIFFRACTION
r_scbond_it
0.88
3
6372
X-RAY DIFFRACTION
r_scangle_it
1.747
4.5
5685
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
3003
tightpositional
0.01
0.05
1
1
D
3003
tightpositional
0.01
0.05
1
1
B
3003
tightpositional
0.01
0.05
1
1
E
3003
tightpositional
0.01
0.05
2
2
C
2926
tightpositional
0.02
0.05
2
2
F
2926
tightpositional
0.02
0.05
1
1
A
3003
tightthermal
0.01
0.5
1
1
D
3003
tightthermal
0.01
0.5
1
1
B
3003
tightthermal
0.01
0.5
1
1
E
3003
tightthermal
0.01
0.5
2
2
C
2926
tightthermal
0.02
0.5
2
2
F
2926
tightthermal
0.02
0.5
LS refinement shell
Resolution: 4.664→4.773 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.455
14
-
Rwork
0.363
187
-
obs
-
-
11.24 %
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
7.7716
-4.1843
2.8685
14.7718
-4.6949
7.9552
0.014
-1.2844
2.4039
0.585
-0.6303
1.0354
-1.017
-0.7325
0.6162
1.1463
0.0564
0.4014
2.1695
-0.7101
1.3056
32.2507
25.5562
78.8763
2
6.5499
2.8065
-2.2665
9.8113
-0.0032
13.9421
-0.166
-0.6187
0.3178
0.949
-0.8045
1.5178
-0.452
-1.6597
0.9705
0.9704
0.7003
0.2109
2.7342
0.0746
2.0284
16.8694
22.6088
85.1574
3
20.4462
-3.5286
-7.2605
6.458
1.6435
9.6728
-0.9417
1.2946
1.53
0.6749
0.5731
-1.2363
0.0944
0.358
0.3687
1.6825
-0.6168
-0.7096
0.6567
0.472
0.8488
62.1737
24.343
73.2866
4
8.0666
-6.0313
0.7419
11.0844
5.3755
13.452
-0.7413
-0.2524
2.4275
0.2734
0.2505
-0.6376
-0.7025
1.8054
0.4908
2.103
-0.6331
0.0463
1.1412
0.327
1.772
67.5656
40.7917
72.2758
5
19.0001
2.3063
2.8914
4.6111
-0.1898
6.4522
-0.0631
0.2846
-0.6509
-1.5959
-0.0383
-1.6331
0.9503
0.8674
0.1014
2.5406
0.6957
0.6238
0.5881
-0.0419
1.0403
75.8306
-16.7424
22.359
6
10.4273
1.8872
-0.8916
9.092
-0.6485
9.2382
-0.2212
0.9505
-0.5324
-0.9769
-0.1806
-0.317
1.3159
0.8334
0.4017
2.2185
0.7646
0.0467
1.2959
-0.0527
1.701
79.5678
-33.1534
21.5821
7
10.6685
-7.2304
-2.9272
15.4641
4.417
7.6615
-0.3248
1.3529
1.3316
-0.0884
0.1139
-0.5115
0.2161
-0.449
0.2109
1.3203
-0.7668
-0.0653
1.4224
0.8237
0.7258
61.472
9.7916
20.6301
8
13.6847
-2.2905
-1.2317
6.9751
1.6983
13.3251
-0.1789
1.4119
0.4097
-0.9445
-1.3788
-0.9204
-0.5398
0.6974
1.5576
1.6665
-0.2408
0.1234
1.0191
0.5219
1.2673
73.1488
20.9265
14.0683
9
12.3928
7.3882
1.4588
14.9052
0.1967
8.8324
-0.4868
-0.5688
-0.3609
1.1212
0.6979
0.6375
1.6484
-0.44
-0.2111
1.5346
1.0161
0.1742
1.3687
0.3034
0.1369
47.0602
-0.8128
81.3724
10
8.2385
0.9864
3.445
7.6105
5.3293
14.8815
0.3684
0.3704
-1.4856
0.2454
-0.4678
0.2193
1.1716
0.0936
0.0994
1.7233
0.4922
-0.244
0.844
0.1544
0.481
58.1331
-13.9493
73.1313
11
9.4297
2.0865
-1.2149
16.4992
-4.9085
8.0528
0.9218
0.6027
-1.1101
0.5331
-1.0907
0.036
0.6821
-1.2212
0.169
1.1409
-0.0656
-0.469
1.698
-0.4946
0.387
45.7552
-15.7251
26.3093
12
5.446
-1.9714
0.092
3.8913
0.7419
18.3046
-1.185
-0.6171
-0.4135
-0.3694
-0.0729
1.2685
0.6694
-1.4636
1.258
0.7785
-0.2865
-0.1804
1.8698
0.2548
0.8061
31.0159
-8.3844
35.1205
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
6 - 79
2
X-RAY DIFFRACTION
1
A
129 - 221
3
X-RAY DIFFRACTION
2
A
80 - 128
4
X-RAY DIFFRACTION
2
A
222 - 419
5
X-RAY DIFFRACTION
3
B
6 - 79
6
X-RAY DIFFRACTION
3
B
129 - 221
7
X-RAY DIFFRACTION
4
B
80 - 128
8
X-RAY DIFFRACTION
4
B
222 - 419
9
X-RAY DIFFRACTION
5
D
6 - 79
10
X-RAY DIFFRACTION
5
D
129 - 221
11
X-RAY DIFFRACTION
6
D
80 - 128
12
X-RAY DIFFRACTION
6
D
222 - 419
13
X-RAY DIFFRACTION
7
E
6 - 79
14
X-RAY DIFFRACTION
7
E
129 - 221
15
X-RAY DIFFRACTION
8
E
80 - 128
16
X-RAY DIFFRACTION
8
E
222 - 419
17
X-RAY DIFFRACTION
9
C
6 - 79
18
X-RAY DIFFRACTION
9
C
129 - 221
19
X-RAY DIFFRACTION
10
C
80 - 128
20
X-RAY DIFFRACTION
10
C
222 - 419
21
X-RAY DIFFRACTION
11
F
6 - 79
22
X-RAY DIFFRACTION
11
F
129 - 221
23
X-RAY DIFFRACTION
12
F
80 - 128
24
X-RAY DIFFRACTION
12
F
222 - 419
+
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