Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE. THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A PRESENCE OF VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION WITH THE PURIFICATION TAG.
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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.03 Details: NANODROP, 52.0% 2-methyl-2,4-pentanediol, 0.1M Citric acid pH 4.03, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.15→29.748 Å / Num. obs: 111860 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.759 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.94
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.15-2.23
0.657
1.2
40676
21162
1
92.5
2.23-2.32
0.547
1.5
42382
21866
1
98.9
2.32-2.42
0.432
1.9
40225
20646
1
99
2.42-2.55
0.312
2.6
43228
22103
1
98.6
2.55-2.71
0.227
3.7
42550
21676
1
98.4
2.71-2.92
0.164
5
42826
21685
1
98.2
2.92-3.21
0.102
8
42128
21249
1
97.8
3.21-3.67
0.055
13.9
42634
21343
1
97.3
3.67-4.61
0.032
22.9
42769
21196
1
96.5
4.61-29.748
0.024
29.1
43233
21163
1
94.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.004
dataextraction
MAR345
CCD
datacollection
XDS
datareduction
SHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.15→29.748 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.471 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. DENSITY FOR LOOP RESIDUES A/B/C/D 59-62 IS POOR. 4. CITRATE, CL, MPD MOLECULES FROM ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. DENSITY FOR LOOP RESIDUES A/B/C/D 59-62 IS POOR. 4. CITRATE, CL, MPD MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. RESIDUAL DENSITIES IN THE ACTIVE SITES WERE MODELED AS UNKNOWN LIGANDS (UNL).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2
5612
5 %
RANDOM
Rwork
0.167
-
-
-
obs
0.168
111840
98.62 %
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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
Displacement parameters
Biso mean: 31.506 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.84 Å2
0 Å2
0 Å2
2-
-
1.11 Å2
0 Å2
3-
-
-
-0.27 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→29.748 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8737
0
145
621
9503
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
9215
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
6267
X-RAY DIFFRACTION
r_angle_refined_deg
1.508
1.983
12576
X-RAY DIFFRACTION
r_angle_other_deg
1.029
3
15247
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.144
5
1136
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.405
23.446
415
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.186
15
1534
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.318
15
68
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
1432
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
10149
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1953
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
1536
X-RAY DIFFRACTION
r_nbd_other
0.195
0.2
6338
X-RAY DIFFRACTION
r_nbtor_refined
0.177
0.2
4342
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
4696
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.18
0.2
517
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.174
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.277
0.2
25
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.248
0.2
64
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.165
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
1.859
3
5752
X-RAY DIFFRACTION
r_mcbond_other
0.516
3
2219
X-RAY DIFFRACTION
r_mcangle_it
2.931
5
9066
X-RAY DIFFRACTION
r_scbond_it
4.719
8
3968
X-RAY DIFFRACTION
r_scangle_it
6.78
11
3490
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
3655
MEDIUMPOSITIONAL
0.25
0.5
1
A
3655
MEDIUMTHERMAL
0.9
2
2
B
3618
MEDIUMPOSITIONAL
0.28
0.5
2
B
3618
MEDIUMTHERMAL
0.92
2
3
A
20
TIGHTPOSITIONAL
0.02
0.05
3
A
20
TIGHTTHERMAL
0.15
0.5
LS refinement shell
Resolution: 2.15→2.207 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.292
401
-
Rwork
0.257
7542
-
all
-
7943
-
obs
-
-
95.33 %
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
0.7244
-0.0984
0.2684
1.224
-0.1679
1.2287
0.0558
0.0536
-0.0748
-0.19
-0.0063
0.207
0.1518
-0.1589
-0.0495
-0.0502
-0.0183
-0.059
0.0377
0.0006
-0.0511
31.8729
21.2651
20.6444
2
1.6653
0.1153
-0.1638
0.4988
-0.156
0.3973
-0.0011
-0.2175
-0.3046
0.068
-0.0234
-0.0485
0.0837
0.0665
0.0245
-0.0309
0.0226
-0.0307
-0.0142
0.0757
-0.0202
54.4527
7.4453
43.9161
3
0.7957
0.1432
-0.4331
0.3467
-0.0948
1.0523
0.0496
0.0526
0.1157
0.0375
-0.0214
0.0009
-0.0443
0.0614
-0.0282
-0.0681
-0.0156
0.0216
-0.072
0.0294
-0.0273
15.2953
21.2785
63.1321
4
1.2908
0.0569
0.4236
0.7665
-0.4877
1.0137
0.0337
0.1959
0.084
-0.0928
0.0423
0.1446
0.0476
0.0606
-0.076
-0.0403
0.0202
-0.0343
-0.0619
0.03
-0.0571
-8.4399
-1.3207
49.7294
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
0 - 273
12 - 285
2
X-RAY DIFFRACTION
1
A
I
300
1
3
X-RAY DIFFRACTION
2
B
B
0 - 273
12 - 285
4
X-RAY DIFFRACTION
3
C
C
-1 - 273
11 - 285
5
X-RAY DIFFRACTION
3
C
N
300
1
6
X-RAY DIFFRACTION
4
D
D
0 - 273
12 - 285
+
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