TLS DETAILS NUMBER OF TLS GROUPS : 18 TLS GROUP : 19 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C ... TLS DETAILS NUMBER OF TLS GROUPS : 18 TLS GROUP : 19 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 1 A 1 RESIDUE RANGE : B 18 B 18 ORIGIN FOR THE GROUP (A): -8.8200 7.1830 18.5870 T TENSOR T11: -0.0519 T22: -0.0267 T33: 0.0385 T12: 0.0394 T13: -0.0319 T23: 0.0779 L TENSOR L11: 14.1366 L22: 11.7182 L33: 4.2157 L12: -1.4888 L13: -6.4616 L23: 1.1182 S TENSOR S11: -0.4483 S12: -1.2562 S13: -0.2132 S21: -0.5346 S22: 0.7290 S23: 0.6125 S31: -0.0260 S32: 0.5428 S33: -0.2808 TLS GROUP : 20 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 2 A 2 RESIDUE RANGE : B 17 B 17 ORIGIN FOR THE GROUP (A): -9.8510 10.0160 16.1620 T TENSOR T11: 0.0618 T22: 0.0150 T33: 0.0336 T12: 0.0005 T13: -0.0092 T23: 0.1532 L TENSOR L11: 15.9283 L22: 27.8775 L33: 9.9726 L12: -11.0879 L13: -9.0205 L23: 14.3390 S TENSOR S11: 0.3958 S12: -0.4326 S13: -0.3760 S21: -0.6098 S22: 0.1489 S23: 0.6202 S31: -0.1389 S32: -0.2975 S33: -0.5447 TLS GROUP : 21 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 3 A 3 RESIDUE RANGE : B 16 B 16 ORIGIN FOR THE GROUP (A): -10.1910 12.9460 13.7150 T TENSOR T11: -0.0179 T22: -0.0258 T33: 0.0665 T12: -0.0341 T13: 0.0043 T23: 0.0581 L TENSOR L11: 8.0179 L22: 4.2885 L33: 13.7466 L12: 1.9119 L13: 2.0030 L23: 2.7726 S TENSOR S11: 0.2204 S12: -0.1382 S13: -0.3021 S21: 0.0477 S22: -0.0126 S23: 0.4627 S31: 0.9454 S32: -0.3193 S33: -0.2078 TLS GROUP : 22 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 4 A 4 RESIDUE RANGE : B 15 B 15 ORIGIN FOR THE GROUP (A): -8.6980 15.8100 11.4540 T TENSOR T11: -0.1034 T22: -0.1096 T33: 0.0163 T12: -0.0867 T13: -0.0150 T23: 0.0586 L TENSOR L11: 14.2712 L22: 9.1272 L33: 13.0762 L12: 8.1245 L13: 8.3756 L23: 4.4191 S TENSOR S11: -0.0699 S12: 0.2076 S13: -0.4628 S21: -0.0698 S22: 0.3285 S23: 0.1541 S31: 0.6432 S32: 0.0607 S33: -0.2587 TLS GROUP : 23 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 5 A 5 RESIDUE RANGE : B 14 B 14 ORIGIN FOR THE GROUP (A): -5.9030 17.0960 8.8580 T TENSOR T11: -0.1003 T22: -0.0312 T33: 0.0165 T12: -0.0099 T13: -0.0097 T23: 0.0419 L TENSOR L11: 10.4040 L22: 0.4045 L33: 2.0592 L12: -0.6052 L13: 2.1545 L23: -0.8971 S TENSOR S11: 0.0810 S12: 0.1737 S13: -0.0476 S21: 0.0359 S22: 0.1777 S23: 0.1903 S31: 0.2348 S32: 0.0430 S33: -0.2587 TLS GROUP : 24 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 6 A 6 RESIDUE RANGE : B 13 B 13 ORIGIN FOR THE GROUP (A): -3.2100 16.9620 5.8750 T TENSOR T11: -0.1161 T22: -0.0992 T33: -0.0105 T12: -0.0165 T13: -0.0078 T23: -0.0219 L TENSOR L11: 2.4593 L22: 5.5141 L33: 3.9213 L12: -3.0189 L13: -1.5248 L23: -0.4479 S TENSOR S11: -0.0587 S12: -0.0207 S13: -0.1416 S21: 0.2278 S22: 0.1527 S23: 0.0541 S31: 0.0852 S32: -0.1081 S33: -0.0940 TLS GROUP : 25 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 7 A 7 RESIDUE RANGE : B 12 B 12 ORIGIN FOR THE GROUP (A): -1.5120 14.7440 3.2050 T TENSOR T11: -0.0158 T22: -0.0849 T33: -0.0189 T12: -0.0105 T13: -0.0475 T23: -0.0454 L TENSOR L11: 7.8751 L22: 6.5666 L33: 3.6804 L12: -6.7783 L13: 2.4894 L23: -3.5984 S TENSOR S11: 0.0417 S12: -0.0303 S13: -0.1646 S21: -0.0313 S22: 0.2035 S23: 0.1687 S31: 0.0968 S32: 0.0260 S33: -0.2452 TLS GROUP : 26 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 8 A 8 RESIDUE RANGE : B 11 B 11 ORIGIN FOR THE GROUP (A): -1.4640 11.9480 0.4300 T TENSOR T11: 0.0450 T22: -0.0649 T33: 0.0035 T12: -0.0415 T13: -0.0712 T23: -0.0422 L TENSOR L11: 4.4328 L22: 13.0940 L33: 12.9403 L12: -2.5463 L13: 0.6691 L23: -12.6048 S TENSOR S11: 0.3532 S12: -0.0516 S13: -0.2391 S21: -0.4567 S22: -0.0446 S23: 0.2498 S31: 1.0755 S32: 0.2924 S33: -0.3085 TLS GROUP : 27 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 9 A 9 RESIDUE RANGE : B 10 B 10 ORIGIN FOR THE GROUP (A): -3.4650 9.2410 -1.7830 T TENSOR T11: 0.0051 T22: -0.0719 T33: 0.0921 T12: -0.0603 T13: -0.0885 T23: -0.0627 L TENSOR L11: 6.9740 L22: 14.3431 L33: 1.2275 L12: -2.9973 L13: 2.5501 L23: -3.0588 S TENSOR S11: 0.3202 S12: 0.1617 S13: -0.6944 S21: 0.4586 S22: 0.3253 S23: -0.0135 S31: 0.2834 S32: 0.3436 S33: -0.6455 TLS GROUP : 28 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 10 A 10 RESIDUE RANGE : B 9 B 9 ORIGIN FOR THE GROUP (A): -6.1240 7.6550 -4.1420 T TENSOR T11: -0.0803 T22: 0.0836 T33: 0.0494 T12: -0.0595 T13: -0.1002 T23: 0.0253 L TENSOR L11: 7.1459 L22: 9.2674 L33: 0.9937 L12: 0.0008 L13: 1.4810 L23: 2.5229 S TENSOR S11: 0.3680 S12: -0.1839 S13: -0.6079 S21: 0.3513 S22: -0.2671 S23: -0.3854 S31: -0.3182 S32: 0.5033 S33: -0.1009 TLS GROUP : 29 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 11 A 11 RESIDUE RANGE : B 8 B 8 ORIGIN FOR THE GROUP (A): -9.2880 7.5890 -6.5580 T TENSOR T11: -0.1326 T22: 0.0042 T33: 0.0594 T12: 0.0242 T13: -0.0717 T23: -0.0629 L TENSOR L11: 7.4564 L22: 11.8118 L33: 3.0967 L12: -3.3750 L13: -0.6497 L23: -2.0931 S TENSOR S11: 0.7084 S12: 0.5031 S13: 0.1893 S21: -0.1568 S22: -0.4749 S23: -0.9273 S31: -0.2426 S32: 0.6932 S33: -0.2335 TLS GROUP : 30 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 12 A 12 RESIDUE RANGE : B 7 B 7 ORIGIN FOR THE GROUP (A): -11.9940 8.9350 -8.9040 T TENSOR T11: -0.1174 T22: -0.0779 T33: 0.0132 T12: 0.0421 T13: -0.0327 T23: -0.0281 L TENSOR L11: 1.4856 L22: 12.4331 L33: 0.6545 L12: 0.0722 L13: -0.4493 L23: 0.5355 S TENSOR S11: -0.0167 S12: -0.1062 S13: -0.0815 S21: 0.4470 S22: 0.3990 S23: 0.1298 S31: -0.0564 S32: 0.1336 S33: -0.3823 TLS GROUP : 31 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 13 A 13 RESIDUE RANGE : B 6 B 6 ORIGIN FOR THE GROUP (A): -13.1080 11.3590 -12.0290 T TENSOR T11: -0.1811 T22: -0.1171 T33: -0.0058 T12: -0.0654 T13: 0.0121 T23: -0.0111 L TENSOR L11: 5.8744 L22: 5.7272 L33: 3.3770 L12: -0.7151 L13: 1.4720 L23: 2.8566 S TENSOR S11: 0.2693 S12: -0.0225 S13: -0.0459 S21: 0.5660 S22: -0.0530 S23: 0.0215 S31: 0.2608 S32: -0.2357 S33: -0.2163 TLS GROUP : 32 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 14 A 14 RESIDUE RANGE : B 5 B 5 ORIGIN FOR THE GROUP (A): -11.6110 13.7960 -14.6430 T TENSOR T11: 0.0377 T22: 0.0045 T33: 0.0462 T12: -0.0653 T13: -0.0615 T23: 0.0191 L TENSOR L11: 23.2118 L22: 24.3718 L33: 6.2589 L12: 22.3271 L13: 11.1429 L23: 12.3412 S TENSOR S11: 0.2578 S12: 0.5855 S13: -0.0770 S21: 0.9721 S22: 0.1334 S23: 0.4012 S31: 0.3259 S32: 1.0778 S33: -0.3912 TLS GROUP : 33 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 15 A 15 RESIDUE RANGE : B 4 B 4 ORIGIN FOR THE GROUP (A): -9.4020 16.0510 -17.2890 T TENSOR T11: -0.1586 T22: -0.1379 T33: -0.0735 T12: 0.0012 T13: 0.0218 T23: 0.0441 L TENSOR L11: 18.4991 L22: 9.4699 L33: 7.8384 L12: 9.9666 L13: 9.9360 L23: 6.1890 S TENSOR S11: 0.3094 S12: 0.7188 S13: -0.2308 S21: 0.4228 S22: -0.0059 S23: -0.0318 S31: 0.4375 S32: 0.7723 S33: -0.3035 TLS GROUP : 34 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 16 A 16 RESIDUE RANGE : B 3 B 3 ORIGIN FOR THE GROUP (A): -6.1200 17.5310 -19.9960 T TENSOR T11: -0.1111 T22: -0.0378 T33: -0.0072 T12: 0.0165 T13: 0.0025 T23: 0.0168 L TENSOR L11: 31.0036 L22: 0.2921 L33: 1.0800 L12: 2.0370 L13: 5.7447 L23: 0.3278 S TENSOR S11: 0.0224 S12: 0.2153 S13: -0.2586 S21: -0.0283 S22: 0.2254 S23: -0.0834 S31: 0.4199 S32: -0.0954 S33: -0.2478 TLS GROUP : 35 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 17 A 17 RESIDUE RANGE : B 2 B 2 ORIGIN FOR THE GROUP (A): -3.3970 16.9530 -23.2680 T TENSOR T11: -0.0772 T22: 0.0305 T33: 0.0662 T12: 0.0132 T13: 0.0301 T23: 0.0003 L TENSOR L11: 6.1503 L22: 4.8385 L33: 0.4192 L12: -2.6607 L13: -1.6028 L23: 0.7660 S TENSOR S11: -0.2331 S12: -0.0752 S13: 0.6094 S21: 0.1883 S22: 0.5087 S23: -0.4581 S31: 0.1606 S32: -0.5986 S33: -0.2756 TLS GROUP : 36 NUMBER OF COMPONENTS GROUP : 2 COMPONENTS C SSSEQI TO C SSSEQI RESIDUE RANGE : A 18 A 18 RESIDUE RANGE : B 1 B 1 ORIGIN FOR THE GROUP (A): -2.1650 15.3180 -26.1940 T TENSOR T11: -0.0191 T22: -0.0692 T33: 0.0706 T12: -0.0071 T13: -0.0324 T23: -0.0525 L TENSOR L11: 5.0650 L22: 1.0127 L33: 4.7334 L12: 1.6469 L13: -2.7360 L23: -2.1360 S TENSOR S11: 0.3081 S12: -0.0535 S13: 0.3060 S21: -0.5620 S22: 0.1701 S23: 0.0099 S31: 0.1114 S32: -0.2038 S33: -0.4782
Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 1.81 Å3/Da / Density % sol: 52.6 % Description: DETERMINED BY MODEL BUILDING IN MAD MAP BUT REFINED AGAINST ONLY THE NATIVE DATA.
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS, NaCl, MgCL2, MPD, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
ID
Name
Crystal-ID
Sol-ID
1
MOPS
1
1
2
NaCl
1
1
3
MgCL2
1
1
4
MPD
1
1
5
H2O
1
1
6
NaCl
1
2
7
MgCL2
1
2
8
MPD
1
2
9
H2O
1
2
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
1,2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength
Wavelength (Å)
SYNCHROTRON
ALS
8.2.1
1
0.886
SYNCHROTRON
ALS
8.2.2
2
0.9198, 0.9204, 0.8856
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Jul 25, 2004
ADSC QUANTUM 4
2
CCD
Apr 5, 2004
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
MAD
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.886
1
2
0.9198
1
3
0.9204
1
4
0.8856
1
Reflection
Resolution: 1.58→19.55 Å / Num. obs: 11050 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.051 / Net I/σ(I): 40.5
Reflection shell
Resolution: 1.58→1.62 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.365 / % possible all: 99.9
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
Blu-Ice
datacollection
SCALEPACK
datascaling
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.58→19.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.17 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT WERE NOT ADDED TO COORDINATES. THERE ARE TWO OVERLAPPED DUPLEXES IN THE ASU, EACH WITH AN OCCUPANCY OF O.5. REMARK 3 CONTAINS TLS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT WERE NOT ADDED TO COORDINATES. THERE ARE TWO OVERLAPPED DUPLEXES IN THE ASU, EACH WITH AN OCCUPANCY OF O.5. REMARK 3 CONTAINS TLS DETAILS FOR MODEL 1 IN THE COORDINATES, REMARK 7 CONTAINS TLS DETAILS FOR MODEL 2 IN THE COORDINATES.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.279
1085
9.8 %
RANDOM
Rwork
0.218
-
-
-
obs
0.224
9965
100 %
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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: 28.437 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.57 Å2
0.29 Å2
0 Å2
2-
-
0.57 Å2
0 Å2
3-
-
-
-0.86 Å2
Refinement step
Cycle: LAST / Resolution: 1.58→19.55 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
750
0
41
791
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.021
1664
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.06
3
2584
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
356
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
720
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.5
221
X-RAY DIFFRACTION
r_nbd_other
0.212
0.5
443
X-RAY DIFFRACTION
r_nbtor_refined
0.315
0.5
576
X-RAY DIFFRACTION
r_nbtor_other
0.065
0.5
313
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.358
0.5
36
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
0.132
0.15
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.174
0.2
8
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.311
0.5
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
1.556
3
2308
X-RAY DIFFRACTION
r_scangle_it
1.895
4.5
2584
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.58→1.62 Å / Total num. of bins used: 20