Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K- ...Details: 2 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K-formate, 26% PEG 3350 and additives of 10 mM L-Met and 1 mM TCEP]; crystal cryoprotected by quick soak in mother liquor supplemented with 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K
Resolution: 2→37.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.108 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20871
2141
5.042 %
RANDOM
Rwork
0.16826
-
-
-
all
0.17
-
-
-
obs
0.17033
42461
99.7 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 38.029 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.2 Å2
0 Å2
0 Å2
2-
-
4.18 Å2
0 Å2
3-
-
-
-2.98 Å2
Refinement step
Cycle: LAST / Resolution: 2→37.16 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4240
0
82
217
4539
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
4467
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
3035
X-RAY DIFFRACTION
r_angle_refined_deg
1.197
1.961
6051
X-RAY DIFFRACTION
r_angle_other_deg
0.849
3.001
7371
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.815
5
539
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.248
24.058
207
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.446
15
757
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.738
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.071
0.2
657
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
4893
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
907
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
1.66
4
2672
X-RAY DIFFRACTION
r_mcbond_other
0.561
4
1078
X-RAY DIFFRACTION
r_mcangle_it
2.397
6
4321
X-RAY DIFFRACTION
r_scbond_it
3.141
6
1795
X-RAY DIFFRACTION
r_scangle_it
4.297
10
1725
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
% reflection obs (%)
WRfactor Rwork
2.004-2.056
0.283
152
0.24
2833
0.242
3096
96.415
0.218
2.056-2.112
0.235
155
0.224
2879
0.225
3038
99.868
0.201
2.112-2.173
0.252
138
0.207
2786
0.209
2925
99.966
0.184
2.173-2.24
0.235
166
0.191
2682
0.194
2852
99.86
0.167
2.24-2.313
0.216
140
0.181
2626
0.183
2770
99.856
0.158
2.313-2.394
0.199
140
0.169
2549
0.171
2690
99.963
0.146
2.394-2.484
0.211
133
0.163
2460
0.166
2593
100
0.141
2.484-2.585
0.265
111
0.174
2367
0.178
2480
99.919
0.151
2.585-2.699
0.185
137
0.16
2287
0.161
2424
100
0.138
2.699-2.83
0.231
102
0.17
2192
0.173
2294
100
0.148
2.83-2.982
0.192
101
0.162
2094
0.164
2196
99.954
0.144
2.982-3.162
0.214
94
0.173
2010
0.175
2104
100
0.154
3.162-3.378
0.238
105
0.173
1841
0.176
1946
100
0.158
3.378-3.647
0.204
91
0.168
1753
0.17
1844
100
0.158
3.647-3.991
0.175
91
0.154
1607
0.155
1698
100
0.15
3.991-4.455
0.169
80
0.136
1470
0.138
1550
100
0.137
4.455-5.132
0.187
62
0.137
1309
0.139
1372
99.927
0.137
5.132-6.256
0.223
65
0.181
1124
0.184
1189
100
0.174
6.256-8.725
0.175
47
0.165
895
0.166
942
100
0.166
8.725-37.165
0.236
31
0.164
556
0.167
587
100
0.185
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
1.355
-0.2506
1.2812
0.9213
-0.8023
2.7103
0.0669
0.1559
-0.2149
-0.1203
-0.08
-0.0558
0.4175
0.0978
0.0131
0.1453
0.0073
0.0189
0.0301
-0.0357
0.1274
26.8531
35.945
-5.8192
2
7.8028
0.6138
1.9602
2.6443
-0.503
2.603
-0.3242
0.6411
0.9595
0.013
-0.0811
-0.2402
-0.4057
0.4332
0.4054
0.1777
-0.0211
-0.0381
0.1252
0.0793
0.2295
27.7332
57.6164
-18.2997
3
1.8752
-0.5606
0.4384
1.7816
0.1958
2.7688
-0.0059
0.0284
0.011
0.0657
-0.0494
0.0509
0.0191
-0.0803
0.0553
0.0453
-0.0073
-0.0011
0.029
-0.0088
0.1079
17.9825
46.8964
-7.0708
4
1.1445
-0.4907
1.3535
0.5566
-0.7088
2.6248
-0.0033
0.0288
0.0572
0.0158
-0.1301
-0.1458
0.0682
0.316
0.1334
0.1174
0.0195
0.0187
0.1046
0.0239
0.1538
36.9901
40.4721
7.7365
5
1.8921
-0.5736
1.5442
1.3261
-0.6788
3.0966
0.095
-0.1443
-0.1371
-0.0325
-0.0473
-0.1595
0.2674
0.1444
-0.0477
0.1334
0.0078
0.0074
0.0552
0.0391
0.1618
41.3906
31.2788
26.8326
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
207 - 325
2
X-RAY DIFFRACTION
2
A
326 - 377
3
X-RAY DIFFRACTION
3
A
378 - 469
4
X-RAY DIFFRACTION
4
A
470 - 601
5
X-RAY DIFFRACTION
5
A
602 - 736
+
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