Mass: 18.015 Da / Num. of mol.: 213 / 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
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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: 2.16 Å3/Da / Density % sol: 43.05 % Description: THE STATISTICS REPORTED IN THE REMARK 200 STATEMENTS ABOVE WERE COMPUTED WITH THE FRIEDEL PAIRS KEPT SEPARATE.
Crystal grow
Temperature: 277 K / pH: 6 Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.55→26.371 Å / Num. obs: 31526 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.87 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.74
Reflection shell
Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.4 / % possible all: 96.2
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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
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.55→26.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 2.999 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.081 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. ACT MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.199
1592
5.1 %
RANDOM
Rwork
0.177
-
-
-
obs
0.178
31524
99.7 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 25.31 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.17 Å2
0 Å2
0 Å2
2-
-
-0.17 Å2
0 Å2
3-
-
-
0.35 Å2
Refinement step
Cycle: LAST / Resolution: 1.55→26.37 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1648
0
4
213
1865
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1825
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
1209
X-RAY DIFFRACTION
r_angle_refined_deg
1.584
1.954
2496
X-RAY DIFFRACTION
r_angle_other_deg
1.239
3
3007
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.387
5
247
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.914
25.824
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.948
15
346
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.708
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
281
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2079
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
339
X-RAY DIFFRACTION
r_nbd_refined
0.185
0.2
315
X-RAY DIFFRACTION
r_nbd_other
0.144
0.2
1184
X-RAY DIFFRACTION
r_nbtor_refined
0.152
0.2
867
X-RAY DIFFRACTION
r_nbtor_other
0.075
0.2
934
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.082
0.2
188
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
0.2
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.146
0.2
42
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.13
0.2
28
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
1.197
2
1190
X-RAY DIFFRACTION
r_mcbond_other
0.2
2
447
X-RAY DIFFRACTION
r_mcangle_it
1.842
4
1838
X-RAY DIFFRACTION
r_scbond_it
3.412
6
749
X-RAY DIFFRACTION
r_scangle_it
4.551
8
638
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.55→1.59 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.257
109
-
Rwork
0.245
2218
-
obs
-
-
99.4 %
Refinement TLS params.
Method: refined / Origin x: 1.481 Å / Origin y: 25.47 Å / Origin z: 5.597 Å
11
12
13
21
22
23
31
32
33
T
-0.0924 Å2
-0.0031 Å2
0.0049 Å2
-
-0.1061 Å2
-0.0041 Å2
-
-
-0.1199 Å2
L
1.4217 °2
-0.0307 °2
0.2912 °2
-
0.3633 °2
-0.0659 °2
-
-
0.494 °2
S
-0.0494 Å °
0.0718 Å °
0.0141 Å °
0.0145 Å °
0.0516 Å °
-0.0351 Å °
-0.061 Å °
0.026 Å °
-0.0022 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
3 - 105
2
X-RAY DIFFRACTION
1
A
113 - 219
+
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