Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
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Details
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: 2.06 Å3/Da / Density % sol: 40.4 %
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 16, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.61→38.778 Å / Num. obs: 93024 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 18.602 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.47
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.61-1.67
0.605
2.32
35959
9731
1
99.6
1.67-1.73
0.474
3
31343
8441
1
99.7
1.73-1.81
0.342
3.9
35530
9551
1
99.7
1.81-1.91
0.235
5.4
36470
9803
1
99.4
1.91-2.03
0.152
7.7
34753
9351
1
99
2.03-2.18
0.107
10.1
33056
8917
1
98.5
2.18-2.4
0.082
12.3
34607
9364
1
98.6
2.4-2.75
0.069
14.1
34929
9410
1
98.2
2.75-3.46
0.053
16.9
33955
9175
1
96.9
3.46-38.778
0.042
19.2
34103
9281
1
95.7
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.4.0067
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.004
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.61→38.778 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.994 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CA IONS, ACETATE IONS AND PEG MOLECULES FROM CRYSTALLIZATION CONDITIONS ARE MODELED INTO THE STRUCTURE. 5.PLP MOLECULE AS ADDITIVE FROM CRYSTALLIZATION WAS MODELED IN THE CONSERVED ACTIVE SITE OF EACH SUBUNIT ACCORDING TO THIS PROTEIN'S SEQUENCE BASED FUNCTION PREDICITION. THE PLP MOLECULE AND LYS 233 FORMED A SCHIFF BASE, WHICH IS REFINED AS THE COVALENT COMPOUND LLP.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.175
4663
5 %
RANDOM
Rwork
0.144
-
-
-
obs
0.146
93023
98.86 %
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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: 16.011 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.55 Å2
0 Å2
-0.14 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.39 Å2
Refinement step
Cycle: LAST / Resolution: 1.61→38.778 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5988
0
60
575
6623
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
6382
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4198
X-RAY DIFFRACTION
r_angle_refined_deg
1.742
1.96
8711
X-RAY DIFFRACTION
r_angle_other_deg
1.088
3
10261
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.958
5
812
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.964
24.453
274
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.167
15
1000
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.686
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
952
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
7233
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1280
X-RAY DIFFRACTION
r_mcbond_it
1.824
3
3988
X-RAY DIFFRACTION
r_mcbond_other
0.564
3
1586
X-RAY DIFFRACTION
r_mcangle_it
2.763
5
6422
X-RAY DIFFRACTION
r_scbond_it
4.898
8
2394
X-RAY DIFFRACTION
r_scangle_it
7.089
11
2289
LS refinement shell
Resolution: 1.61→1.652 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.256
324
-
Rwork
0.181
6629
-
all
-
6953
-
obs
-
-
99.93 %
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
0.4959
-0.1269
0.1498
0.3595
0.0118
0.366
-0.0082
-0.0357
0.0206
0.0279
-0.0056
0.0361
-0.0206
-0.0449
0.0138
-0.0304
0.0192
0.0053
-0.029
-0.0022
-0.0255
7.1343
15.2631
25.0053
2
0.1466
-0.0751
-0.0452
0.1302
0.0545
0.3643
0.0328
0.0353
-0.0143
-0.0511
-0.0195
-0.0339
0.0152
0.0252
-0.0133
0.0019
0.0217
-0.0014
-0.0162
-0.0155
-0.0213
30.9214
-6.6537
7.4409
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
4 - 389
5 - 390
2
X-RAY DIFFRACTION
2
B
B
4 - 388
5 - 389
+
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