SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ... SEQUENCE A 25-AA N-TERMINAL TAG WAS CLEAVED BY THROMBIN. IN RESULT, THE FINAL PURIFIED PROTEIN HAD ONLY MODIFICATION FOR ITS METHIONINE RESIDUES TO SE-MET RESIDUES.
A: Conserved protein MTH889 B: Conserved protein MTH889 C: Conserved protein MTH889 D: Conserved protein MTH889 E: Conserved protein MTH889 F: Conserved protein MTH889 G: Conserved protein MTH889 hetero molecules
A: Conserved protein MTH889 B: Conserved protein MTH889 C: Conserved protein MTH889 D: Conserved protein MTH889 E: Conserved protein MTH889 F: Conserved protein MTH889 G: Conserved protein MTH889 hetero molecules
A: Conserved protein MTH889 B: Conserved protein MTH889 C: Conserved protein MTH889 D: Conserved protein MTH889 E: Conserved protein MTH889 F: Conserved protein MTH889 G: Conserved protein MTH889 hetero molecules
Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal grow
Temperature: 291 K / Method: microbatch under oil / pH: 7.5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 7.5, 18% PEG 400, 200 mM CaCl2, 3% 1,6-Hexanediol, MICROBATCH UNDER OIL, temperature 291K
Resolution: 3.1→3.21 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 6.13 / Num. unique all: 2573 / Rsym value: 0.282 / % possible all: 99.8
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0003
refinement
ADSC
Quantum
datacollection
DENZO
datareduction
SCALEPACK
datascaling
SnB
phasing
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 3.11→80.58 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.862 / SU B: 43.319 / SU ML: 0.386 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS_1.2 has also been used in refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2802
691
4.9 %
RANDOM
Rwork
0.21559
-
-
-
all
0.22
25802
-
-
obs
0.21871
13283
99.4 %
-
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: 55.914 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1 Å2
0 Å2
0 Å2
2-
-
0.1 Å2
0 Å2
3-
-
-
-0.2 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.48 Å
0.44 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.71 Å
0.57 Å
Refinement step
Cycle: LAST / Resolution: 3.11→80.58 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5082
0
14
54
5150
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
5152
X-RAY DIFFRACTION
r_angle_refined_deg
1.774
1.979
6989
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.979
5
645
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
43.678
25.625
224
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
24.829
15
960
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.343
15
28
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
849
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3777
X-RAY DIFFRACTION
r_nbd_refined
0.289
0.2
2730
X-RAY DIFFRACTION
r_nbtor_refined
0.336
0.2
3510
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.205
0.2
222
X-RAY DIFFRACTION
r_metal_ion_refined
0.133
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.292
0.2
100
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.17
0.2
3
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.196
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
0.694
1.5
3306
X-RAY DIFFRACTION
r_mcangle_it
1.255
2
5315
X-RAY DIFFRACTION
r_scbond_it
2.258
3
2008
X-RAY DIFFRACTION
r_scangle_it
3.349
4.5
1674
LS refinement shell
Resolution: 3.11→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.286
50
-
Rwork
0.225
938
-
obs
-
938
98.02 %
Refinement TLS params.
Method: refined / Origin x: 19.4402 Å / Origin y: 75.2137 Å / Origin z: -7.4043 Å
11
12
13
21
22
23
31
32
33
T
-0.1003 Å2
-0.0445 Å2
0.0071 Å2
-
-0.0905 Å2
-0.0192 Å2
-
-
-0.1372 Å2
L
0.5902 °2
0.3815 °2
-0.1039 °2
-
0.5738 °2
-0.1203 °2
-
-
0.0658 °2
S
-0.09 Å °
0.0836 Å °
-0.0714 Å °
-0.079 Å °
0.0839 Å °
-0.0015 Å °
0.0212 Å °
-0.0681 Å °
0.0061 Å °
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
3 - 95
3 - 95
2
X-RAY DIFFRACTION
1
B
B
2 - 95
2 - 95
3
X-RAY DIFFRACTION
1
C
C
3 - 95
3 - 95
4
X-RAY DIFFRACTION
1
D
D
3 - 95
3 - 95
5
X-RAY DIFFRACTION
1
E
E
3 - 95
3 - 95
6
X-RAY DIFFRACTION
1
F
F
3 - 95
3 - 95
7
X-RAY DIFFRACTION
1
G
G
3 - 95
3 - 95
+
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