HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR ...HETEROGEN THE PALMITIC ACID (PLM) AND ACETAMIDE (ACM) GROUPS ARE COVALENTLY LINKED TO THEIR RESPECTIVE CYSTEINE RESIDUES.
Remark 999
SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED ...SEQUENCE THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ORIGINAL SEQUENCE DATABASE RESIDUE NUMBERS (2-161) OF THE LYSOZYME PART IN COORDINATES TO DISTINGUISH THE LYSOZYME PART IN THE CHAIN. THEREFORE THE RESIDUES OF LYSOZYME PART HAVE NUMBERS A1002-A1161.
Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 27
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Sample preparation
Crystal
Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % Description: This structure is a part of the Roadmap/PSI community outreach program, not a specific PSI target.
Crystal grow
Temperature: 293 K / Method: lipidic mesophase / pH: 6.75 Details: 30-35% v/v PEG 400, 0.1-0.2 M Na2SO4, 0.1 M Bis-tris propane pH 6.5-7.0, 5-7% 1,4-Butanediol, 8-10% Cholesterol, 52-50% Monoolein, pH 6.75, LIPIDIC MESOPHASE, temperature 293K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
78
1
2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
APS
23-ID-B
1
1.03321
SYNCHROTRON
APS
23-ID-B
2
1.03321
Detector
Type
ID
Detector
Date
Details
MARMOSAIC 300 mm CCD
1
CCD
Jun 22, 2007
mirrors
MARMOSAIC 300 mm CCD
2
CCD
Jul 18, 2007
mirrors
Radiation
Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.03321 Å / Relative weight: 1
Reflection
Resolution: 2.4→20 Å / Num. all: 26705 / Num. obs: 26506 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.908 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.62
Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.501 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Water #548 has strong difference density but weak 2Fo-Fc density.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.232
1310
4.9 %
RANDOM
Rwork
0.196
-
-
-
all
0.198
26506
-
-
obs
0.198
26506
99.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 63.912 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.43 Å2
0 Å2
2.26 Å2
2-
-
-3.46 Å2
0 Å2
3-
-
-
4.25 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→19.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3543
0
213
48
3804
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
3843
X-RAY DIFFRACTION
r_bond_other_d
0
0.02
2622
X-RAY DIFFRACTION
r_angle_refined_deg
1.5
2
5219
X-RAY DIFFRACTION
r_angle_other_deg
4.099
3.002
6377
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.876
5
441
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.604
23.182
154
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.383
15
627
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.164
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
610
X-RAY DIFFRACTION
r_gen_planes_refined
0.001
0.02
4008
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
804
X-RAY DIFFRACTION
r_nbd_refined
0.187
0.3
926
X-RAY DIFFRACTION
r_nbd_other
0.194
0.3
2443
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.5
1935
X-RAY DIFFRACTION
r_nbtor_other
0.107
0.5
1580
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.164
0.5
194
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.155
0.3
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.14
0.3
29
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.192
0.5
6
X-RAY DIFFRACTION
r_mcbond_it
2.352
2
2884
X-RAY DIFFRACTION
r_mcbond_other
0.097
2
896
X-RAY DIFFRACTION
r_mcangle_it
2.767
2.5
3571
X-RAY DIFFRACTION
r_scbond_it
4.582
2
1974
X-RAY DIFFRACTION
r_scangle_it
5.849
2.5
1648
LS refinement shell
Resolution: 2.4→2.461 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.301
78
-
Rwork
0.27
1829
-
all
-
1907
-
obs
-
-
98.76 %
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
3.122
0.8643
0.6146
2.6914
-0.8632
5.9787
-0.1453
-0.2225
0.2116
0.0984
-0.0656
-0.0133
-0.1849
-0.1761
0.2109
-0.2208
0.0432
-0.0594
-0.2598
-0.0241
-0.7033
-23.684
58.405
30.485
2
9.6406
-6.5961
-0.9803
16.6501
3.2882
7.1133
-0.1628
-0.1008
0.4114
-0.7585
-0.1058
0.7355
-0.659
-0.6073
0.2686
0.0414
0.0577
-0.1559
-0.0871
-0.0085
-0.4908
-35.058
69.001
11.961
3
2.367
2.1068
0.8591
6.1551
0.7864
1.9314
-0.0346
0.0267
-0.2068
-0.5009
0.0712
0.2388
0.3208
0.0002
-0.0366
-0.0103
-0.0025
-0.0974
-0.2341
-0.0034
-0.5401
-33.074
20.013
7.122
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
1002 - 1011
238 - 247
2
X-RAY DIFFRACTION
1
A
A
1062 - 1161
298 - 397
3
X-RAY DIFFRACTION
2
A
A
1012 - 1061
248 - 297
4
X-RAY DIFFRACTION
3
A
A
29 - 230
36 - 237
5
X-RAY DIFFRACTION
3
A
A
263 - 342
398 - 477
+
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