Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NANODROP, 40.0% MPD, 5.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.64→28.194 Å / Num. obs: 29308 / % possible obs: 98.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.775 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6.5
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.64-1.68
3.9
0.792
0.9
8153
2099
0.792
96.8
1.68-1.73
3.9
0.597
1.2
8097
2088
0.597
97.1
1.73-1.78
3.9
0.471
1.6
7863
2028
0.471
97.2
1.78-1.83
3.9
0.371
2
7667
1979
0.371
97.5
1.83-1.89
3.9
0.278
2.7
7461
1923
0.278
97.6
1.89-1.96
3.9
0.209
3.5
7140
1846
0.209
97.8
1.96-2.03
3.9
0.155
4.7
7040
1818
0.155
98
2.03-2.12
3.9
0.129
5.5
6743
1745
0.129
98.2
2.12-2.21
3.9
0.113
6.3
6364
1642
0.113
98.2
2.21-2.32
3.9
0.096
7.3
6158
1595
0.096
98.5
2.32-2.44
3.9
0.086
8
5897
1526
0.086
98.6
2.44-2.59
3.9
0.08
8.3
5529
1431
0.08
98.7
2.59-2.77
3.9
0.072
9.1
5271
1368
0.072
98.8
2.77-2.99
3.8
0.064
10
4841
1261
0.064
99
2.99-3.28
3.8
0.057
10.6
4516
1180
0.057
99.2
3.28-3.67
3.8
0.051
12.3
4029
1058
0.051
99.3
3.67-4.23
3.8
0.045
13.7
3623
954
0.045
99.4
4.23-5.19
3.8
0.043
14.3
2983
795
0.043
99.7
5.19-7.33
3.7
0.048
13.4
2321
629
0.048
99.6
7.33-28.194
3.5
0.051
11.9
1187
343
0.051
95.5
-
Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.64→28.194 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.814 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 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. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO NI ATOMS OF THE A SUBUNIT WERE FOUND IN THE ASYMMETRIC UNIT. THE FIRST NI ATOM WAS COORDINATED TO THE SIDE CHAIN OF HIS 188, GLU 192, AND THREE WATERS. THE OTHER NI ATOM WAS DISORDERED AND DUAL CONFORMATION WERE MODELED. DUAL NI ATOMS WERE COORDINATED TO THE SIDE CHAINS OF HIS 104, HIS 158, GLU 103 AND FOUR WATER MOLECULES. ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE NI IONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2
1491
5.1 %
RANDOM
Rwork
0.165
-
-
-
obs
0.167
29307
97.85 %
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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: 20.725 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.18 Å2
0 Å2
-1.33 Å2
2-
-
-0.19 Å2
0 Å2
3-
-
-
-0.89 Å2
Refinement step
Cycle: LAST / Resolution: 1.64→28.194 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1664
0
2
174
1840
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1804
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1195
X-RAY DIFFRACTION
r_angle_refined_deg
1.561
1.964
2462
X-RAY DIFFRACTION
r_angle_other_deg
0.981
3
2940
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.478
5
231
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.041
24.937
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.441
15
312
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.299
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
272
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2051
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
363
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
379
X-RAY DIFFRACTION
r_nbd_other
0.187
0.2
1268
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
899
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
907
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.164
0.2
139
X-RAY DIFFRACTION
r_metal_ion_refined
0.149
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.199
0.2
16
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.296
0.2
54
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.087
0.2
21
X-RAY DIFFRACTION
r_mcbond_it
2.481
3
1215
X-RAY DIFFRACTION
r_mcbond_other
0.568
3
449
X-RAY DIFFRACTION
r_mcangle_it
3.039
5
1812
X-RAY DIFFRACTION
r_scbond_it
5.609
8
768
X-RAY DIFFRACTION
r_scangle_it
7.574
11
650
LS refinement shell
Resolution: 1.64→1.683 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.384
100
-
Rwork
0.262
1998
-
all
-
2098
-
obs
-
-
96.55 %
Refinement TLS params.
Method: refined / Origin x: 25.5858 Å / Origin y: 33.1978 Å / Origin z: 14.228 Å
11
12
13
21
22
23
31
32
33
T
-0.0643 Å2
0.0002 Å2
0.0244 Å2
-
-0.0506 Å2
-0.0075 Å2
-
-
-0.0729 Å2
L
1.3315 °2
-0.6809 °2
1.3495 °2
-
1.3942 °2
-0.6337 °2
-
-
1.6335 °2
S
0.1014 Å °
0.0947 Å °
-0.0553 Å °
-0.0166 Å °
-0.0271 Å °
0.0896 Å °
0.0595 Å °
-0.0054 Å °
-0.0743 Å °
+
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