Mass: 18.015 Da / Num. of mol.: 200 / 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: 1
-
Sample preparation
Crystal
Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal grow
Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1 UL OF PROTEIN AT 15 MG/ML WITH 1 UL OF 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE PH 5.6, 23-25% (V/V) PEG 4000
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9762 Å / Relative weight: 1
Reflection
Resolution: 1.598→56.841 Å / Num. obs: 58008 / % possible obs: 94.71 % / Redundancy: 2.2 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.055 / Net I/σ(I): 13.4
Reflection shell
Resolution: 1.598→2 Å
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Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.598→56.841 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.88 Details: THE REFINEMENT OF METAL SOAKED FLV1 FLAVODIIRON CORE FROM SYNECHOCYSTIS CONVERGED TO RWORK AND RFREE OF 0.165 AND 0.206, RESPECTIVELY, USING A RFREE TEST SET SIZE OF 1.56% (905 REFLECTIONS). ...Details: THE REFINEMENT OF METAL SOAKED FLV1 FLAVODIIRON CORE FROM SYNECHOCYSTIS CONVERGED TO RWORK AND RFREE OF 0.165 AND 0.206, RESPECTIVELY, USING A RFREE TEST SET SIZE OF 1.56% (905 REFLECTIONS). THE FINAL MODEL THEN WAS REFINED VERSUS THE FULL DATA, RESULTING A FINAL R VALUE OF 0.159.
Rfactor
Num. reflection
% reflection
Rfree
0.1585
905
100 %
Rwork
0.1585
-
-
obs
0.1585
57979
94.71 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 1.598→56.841 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3103
0
11
200
3314
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
3201
X-RAY DIFFRACTION
f_angle_d
1.296
4356
X-RAY DIFFRACTION
f_dihedral_angle_d
14.721
1155
X-RAY DIFFRACTION
f_chiral_restr
0.05
488
X-RAY DIFFRACTION
f_plane_restr
0.005
571
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.5984-1.6165
0.4102
1761
0.4102
1761
X-RAY DIFFRACTION
86
1.6165-1.6356
0.4
1927
0.4
1927
X-RAY DIFFRACTION
96
1.6356-1.6555
0.39
1958
0.39
1958
X-RAY DIFFRACTION
96
1.6555-1.6765
0.3864
1947
0.3864
1947
X-RAY DIFFRACTION
96
1.6765-1.6985
0.3788
1930
0.3788
1930
X-RAY DIFFRACTION
94
1.6985-1.7218
0.3563
1899
0.3563
1899
X-RAY DIFFRACTION
95
1.7218-1.7464
0.3571
1977
0.3571
1977
X-RAY DIFFRACTION
96
1.7464-1.7725
0.3293
1940
0.3293
1940
X-RAY DIFFRACTION
96
1.7725-1.8002
0.3204
1971
0.3204
1971
X-RAY DIFFRACTION
97
1.8002-1.8297
0.3233
1984
0.3233
1984
X-RAY DIFFRACTION
96
1.8297-1.8612
0.2916
1944
0.2916
1944
X-RAY DIFFRACTION
96
1.8612-1.8951
0.2882
1939
0.2882
1939
X-RAY DIFFRACTION
96
1.8951-1.9315
0.2584
1977
0.2584
1977
X-RAY DIFFRACTION
96
1.9315-1.971
0.2561
1941
0.2561
1941
X-RAY DIFFRACTION
96
1.971-2.0138
0.2434
1933
0.2434
1933
X-RAY DIFFRACTION
95
2.0138-2.0607
0.2405
1939
0.2405
1939
X-RAY DIFFRACTION
94
2.0607-2.1122
0.2212
1924
0.2212
1924
X-RAY DIFFRACTION
96
2.1122-2.1693
0.2171
1979
0.2171
1979
X-RAY DIFFRACTION
97
2.1693-2.2331
0.2107
1968
0.2107
1968
X-RAY DIFFRACTION
95
2.2331-2.3052
0.1939
1935
0.1939
1935
X-RAY DIFFRACTION
96
2.3052-2.3876
0.1912
1942
0.1912
1942
X-RAY DIFFRACTION
96
2.3876-2.4832
0.1832
1944
0.1832
1944
X-RAY DIFFRACTION
95
2.4832-2.5962
0.1744
1929
0.1744
1929
X-RAY DIFFRACTION
94
2.5962-2.7331
0.1684
1912
0.1684
1912
X-RAY DIFFRACTION
94
2.7331-2.9043
0.1505
1991
0.1505
1991
X-RAY DIFFRACTION
96
2.9043-3.1286
0.1385
1902
0.1385
1902
X-RAY DIFFRACTION
94
3.1286-3.4434
0.1159
1934
0.1159
1934
X-RAY DIFFRACTION
94
3.4434-3.9415
0.0993
1855
0.0993
1855
X-RAY DIFFRACTION
91
3.9415-4.9655
0.0777
1901
0.0777
1901
X-RAY DIFFRACTION
92
4.9655-56.8768
0.0943
1896
0.0943
1896
X-RAY DIFFRACTION
90
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
0.5865
0.3444
-0.2408
0.2779
-0.1011
0.5383
-0.0887
0.1972
0.0162
-0.0655
0.2366
-0.0739
0.0442
-0.0402
0.0001
0.3092
0.0248
0.0109
0.3358
-0.017
0.2754
13.7008
49.5773
34.1344
2
0.4851
-0.005
0.003
0.3224
0.0913
0.5811
-0.0627
0.0949
0.1103
0.0405
0.1829
-0.2511
-0.0959
0.0856
-0.0001
0.237
-0.0003
0.0349
0.2679
-0.0218
0.3536
19.9197
60.2481
40.4059
3
0.0181
0.0055
-0.0309
0.0192
-0.0125
0.0571
0.0221
-0.2506
0.2209
0.1642
0.3061
-0.4251
-0.0636
0.3611
0.0001
0.2808
-0.0026
0.0722
0.3675
-0.1348
0.5225
29.1374
58.8105
42.495
4
0.2432
0.0288
-0.0183
0.3254
0.0257
0.1065
-0.0796
-0.5567
0.257
0.5598
0.226
-0.5313
-0.1442
0.3341
0.0033
0.3724
0.0238
-0.1036
0.4121
-0.1224
0.4989
26.5183
59.0669
53.3414
5
1.412
0.1557
-0.0389
0.7999
-0.1182
0.499
-0.0089
-0.017
0.0231
0.0879
0.1065
0.0311
-0.0149
-0.3105
0.0007
0.2456
0.0638
0.0151
0.3011
-0.0014
0.2467
6.9001
52.8588
46.1116
6
0.1192
0.0451
0.0935
0.2108
0.0176
0.0708
-0.0152
0.0752
0.0968
0.0867
0.1059
0.0024
0.043
-0.3655
-0
0.2801
0.0807
0.0435
0.4013
0.0097
0.2761
1.5468
54.2672
50.7893
7
0.1174
0.0081
0.1143
0.2319
-0.049
0.1071
-0.001
-0.0073
0.234
-0.1826
0.0631
0.0292
0.0544
-0.2876
0.0001
0.1788
0.0372
-0.0153
0.4299
-0.0021
0.2846
-1.4453
51.0856
41.0824
8
0.145
-0.2045
0.1942
0.7462
-0.734
1.3158
0.0236
0.0701
0.0131
0.0714
-0.0083
-0.0623
0.2482
-0.0906
0.0001
0.3331
-0.0186
-0.0242
0.2597
-0.0267
0.2812
13.7457
34.398
57.102
9
0.2112
-0.2217
0.0627
0.3315
0.0429
0.1007
0.1931
0.029
0.0796
0.1532
-0.0156
-0.1363
0.7775
0.1594
0.0142
0.4358
0.0133
-0.0555
0.3297
-0.0042
0.3656
20.8468
26.1877
60.5557
10
0.2337
-0.1383
0.0364
0.7296
0.2581
0.5018
0.1549
0.2094
-0.3323
-0.1736
-0.0186
-0.1472
0.8451
0.1508
0.0021
0.5961
0.0426
-0.0584
0.3032
-0.0442
0.3898
18.7689
23.1242
52.8205
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid28:60)
2
X-RAY DIFFRACTION
2
(chainAandresid61:114)
3
X-RAY DIFFRACTION
3
(chainAandresid115:123)
4
X-RAY DIFFRACTION
4
(chainAandresid124:154)
5
X-RAY DIFFRACTION
5
(chainAandresid155:234)
6
X-RAY DIFFRACTION
6
(chainAandresid235:253)
7
X-RAY DIFFRACTION
7
(chainAandresid254:268)
8
X-RAY DIFFRACTION
8
(chainAandresid269:355)
9
X-RAY DIFFRACTION
9
(chainAandresid356:377)
10
X-RAY DIFFRACTION
10
(chainAandresid378:428)
+
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