Mass: 44875.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0820 / Production host: Escherichia coli (E. coli) References: UniProt: Q9WZS7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.000034 Å / Relative weight: 1
Reflection
Resolution: 1.78→50 Å / Num. obs: 65785 / % possible obs: 93.95 % / Redundancy: 2.85 % / Biso Wilson estimate: 36.93 Å2 / Rsym value: 0.041 / Net I/σ(I): 21.67
Reflection shell
Resolution: 1.78→1.84 Å / Redundancy: 1.87 % / Mean I/σ(I) obs: 1.94 / Num. unique all: 4773 / Rsym value: 0.338 / % possible all: 68.72
-
Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
EPMR
phasing
REFMAC
5.1.9999
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)
Resolution: 1.78→49.6 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.628 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE MODEL OF THE ACTIVE SITE AROUND THE METAL (FE) IS APPARENTLY STILL INCOMPLETE, AND POSSIBLY A SUPERPOSITION OF STATES: THE METAL (FE) AND THE NAP ARE PARTIALLY OCCUPIED. OMIT DENSITY FOR THE NICOTINAMIDE RING IS WEAK. RESIDUAL DIFFERENCE DENSITY PEAKS PERSIST NEAR NICOTINAMIDE NC5 ATOM AND H272 IN BOTH CHAINS (WEAKER IN B). ONLY ONE STATE, THE MOST DEFENSIBLE ONE, HAS BEEN MODELLED. UNACCOUNTED TUBULAR DENSITY NEXT TO RESIDUES 222 AND 311 IN BOTH CHAINS. UNACCOUNTED STRONG POSITIVE DENSITY NEAR A7/B20 AND B7/A20
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19265
3343
5.1 %
RANDOM
Rwork
0.14224
-
-
-
obs
0.14475
62407
93.86 %
-
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: 35.944 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.38 Å2
0 Å2
1.73 Å2
2-
-
-0.47 Å2
0 Å2
3-
-
-
1.66 Å2
Refinement step
Cycle: LAST / Resolution: 1.78→49.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6078
0
98
480
6656
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
6331
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
5827
X-RAY DIFFRACTION
r_angle_refined_deg
1.562
1.962
8592
X-RAY DIFFRACTION
r_angle_other_deg
1
3
13524
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.671
5
794
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.7
24.444
252
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.591
15
1062
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.307
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.099
0.2
968
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
6972
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1216
X-RAY DIFFRACTION
r_nbd_refined
0.234
0.2
1362
X-RAY DIFFRACTION
r_nbd_other
0.18
0.2
5966
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
3503
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.15
0.2
386
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.061
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.211
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.265
0.2
49
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.16
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
2.249
3
4272
X-RAY DIFFRACTION
r_mcbond_other
0.617
3
1648
X-RAY DIFFRACTION
r_mcangle_it
2.962
5
6342
X-RAY DIFFRACTION
r_scbond_it
5.538
8
2673
X-RAY DIFFRACTION
r_scangle_it
7.306
11
2250
LS refinement shell
Resolution: 1.78→1.826 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.29
180
5.4 %
Rwork
0.234
3155
-
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
0.8033
0.0598
-0.1393
0.3727
0.2049
0.3259
0.0174
-0.0352
0.0314
0.0915
-0.0187
0.0357
-0.0383
0.0299
0.0013
-0.0893
0.0005
0.0053
-0.1697
0.0075
-0.1885
14.0751
44.9107
49.0548
2
0.8989
0.2444
-0.0172
0.3678
0.0151
0.3341
-0.0372
0.1976
-0.0401
-0.0067
0.0461
-0.0519
-0.0164
0.0452
-0.0089
-0.1668
-0.004
0.002
-0.0874
0.0074
-0.2082
25.1932
38.4759
27.1235
3
0.773
-0.0607
0.1355
0.9913
-0.2555
0.2951
-0.0252
-0.0407
-0.0877
0.198
0.0265
0.0133
-0.0317
-0.0226
-0.0012
-0.0811
0.0226
0.0204
-0.172
-0.0123
-0.1332
9.1428
9.672
52.5694
4
1.0045
-0.2658
0.0734
0.5057
-0.0853
0.0468
0.0347
0.1796
-0.235
-0.0153
-0.0479
0.084
-0.0088
-0.0169
0.0132
-0.1586
0.0288
-0.0015
-0.0931
-0.0705
-0.1238
-1.6843
11.4985
29.6976
5
7.9466
-7.1836
-0.5392
6.8608
-0.2672
1.5888
0.3058
-0.1358
0.0602
-0.1
-0.0038
-0.2813
-0.0749
-0.1291
-0.302
-0.0701
-0.0634
-0.0205
-0.1193
0.0572
-0.0787
16.5405
48.287
37.9177
6
9.4973
-1.6316
4.8206
6.3627
-1.9228
2.6438
-0.2048
0.2906
-1.4114
1.0267
0.2584
1.2288
-0.4841
0.1775
-0.0536
-0.0499
-0.0211
0.1104
-0.0887
-0.0455
0.046
6.9661
3.9547
42.4205
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: ALL
ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
1
A
A
1 - 185
13 - 197
2
2
A
A
186 - 394
198 - 406
3
3
B
B
1 - 185
13 - 197
4
4
B
B
186 - 394
198 - 406
5
5
A
C - E
400 - 800
1
6
6
B
D - F
400 - 800
1
+
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