Mass: 36587.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2-155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A0R2V4
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Non-polymers , 6 types, 527 molecules
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
FMN IS THE ONLY BIOLOGICAL RELAVENT HETROGEN IN THIS ENTRY. ALL OTHER HETATOMS ARE COMPONENTS OF ...FMN IS THE ONLY BIOLOGICAL RELAVENT HETROGEN IN THIS ENTRY. ALL OTHER HETATOMS ARE COMPONENTS OF THE CRYSTALLISATION MIX AND IN THE AUTHORS' OPINION, NO BIOLOGICAL ROLE.
Sequence details
EXTRA SER ON THE N-TERMINUS FROM TEV CLEAVAGE SITE
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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: 4.82 Å3/Da / Density % sol: 74.1 % Description: STRUCTURE ORIGINALY SOLVED USING AUTO-RICKSHAW AND 2.4 A DATASET.
Crystal grow
pH: 6.5 Details: 0.1M IMIDAZOLE/MES PH 6.5, 30%(V/V)PEG550MME, 25 MM NA FORMATE, 25 MM AM ACETATE, 25 MM NA CITRATE, 25 MM NAK TARTRATE
Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9148 Å / Relative weight: 1
Reflection
Resolution: 1.6→26.57 Å / Num. obs: 92796 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4
Reflection shell
Resolution: 1.6→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD MODEL AT 2.4 A FROM ANOTHER DATASET Resolution: 1.6→26.568 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 12.95 / Stereochemistry target values: ML Details: RESIDUES 1-2 AND 330 DISORDERED LOOP 292-294 IN MULTIPLE CONFORMATIONS
Rfactor
Num. reflection
% reflection
Rfree
0.147
4626
5 %
Rwork
0.1188
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-
obs
0.1202
92766
99.31 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 21.96 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→26.568 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2533
0
73
518
3124
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.019
2759
X-RAY DIFFRACTION
f_angle_d
1.721
3772
X-RAY DIFFRACTION
f_dihedral_angle_d
13.035
1051
X-RAY DIFFRACTION
f_chiral_restr
0.107
430
X-RAY DIFFRACTION
f_plane_restr
0.01
497
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.6-1.6182
0.2486
158
0.1949
2982
X-RAY DIFFRACTION
100
1.6182-1.6372
0.1902
151
0.1828
2935
X-RAY DIFFRACTION
100
1.6372-1.6572
0.2184
154
0.1719
2915
X-RAY DIFFRACTION
100
1.6572-1.6781
0.2115
154
0.1686
2963
X-RAY DIFFRACTION
100
1.6781-1.7002
0.1822
156
0.1551
2953
X-RAY DIFFRACTION
100
1.7002-1.7235
0.1902
151
0.1489
2879
X-RAY DIFFRACTION
100
1.7235-1.7481
0.2007
156
0.1413
2968
X-RAY DIFFRACTION
100
1.7481-1.7742
0.1698
152
0.1383
2920
X-RAY DIFFRACTION
100
1.7742-1.8019
0.1942
156
0.1367
2935
X-RAY DIFFRACTION
100
1.8019-1.8315
0.1841
155
0.1228
2977
X-RAY DIFFRACTION
100
1.8315-1.863
0.1524
154
0.1163
2892
X-RAY DIFFRACTION
100
1.863-1.8969
0.1537
155
0.1067
2947
X-RAY DIFFRACTION
100
1.8969-1.9334
0.1485
154
0.105
2952
X-RAY DIFFRACTION
100
1.9334-1.9728
0.1293
156
0.1047
2942
X-RAY DIFFRACTION
100
1.9728-2.0157
0.1432
155
0.1018
2943
X-RAY DIFFRACTION
100
2.0157-2.0626
0.1216
151
0.1007
2912
X-RAY DIFFRACTION
100
2.0626-2.1142
0.1386
154
0.0976
2974
X-RAY DIFFRACTION
99
2.1142-2.1713
0.1312
152
0.0948
2898
X-RAY DIFFRACTION
99
2.1713-2.2352
0.129
154
0.0898
2927
X-RAY DIFFRACTION
100
2.2352-2.3073
0.1116
154
0.0878
2971
X-RAY DIFFRACTION
100
2.3073-2.3897
0.1295
153
0.0891
2908
X-RAY DIFFRACTION
99
2.3897-2.4853
0.1306
155
0.0948
2950
X-RAY DIFFRACTION
99
2.4853-2.5983
0.1209
153
0.0939
2960
X-RAY DIFFRACTION
99
2.5983-2.7352
0.1337
153
0.106
2925
X-RAY DIFFRACTION
99
2.7352-2.9063
0.1397
158
0.1171
2943
X-RAY DIFFRACTION
99
2.9063-3.1304
0.1454
154
0.1297
2963
X-RAY DIFFRACTION
99
3.1304-3.4448
0.1571
155
0.1301
2942
X-RAY DIFFRACTION
99
3.4448-3.9419
0.1355
155
0.1222
2955
X-RAY DIFFRACTION
98
3.9419-4.9611
0.1266
157
0.1124
2945
X-RAY DIFFRACTION
98
4.9611-26.5716
0.1766
151
0.1603
2864
X-RAY DIFFRACTION
93
+
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