Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979147 Å / Relative weight: 1
Reflection
Resolution: 3.8→40 Å / Num. obs: 47973 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 172.82 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shell
Resolution: 3.8→3.94 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 96
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 3.8→33.388 Å / SU ML: 0.83 / σ(F): 1.96 / Phase error: 39.94 / Stereochemistry target values: ML Details: MODELLING WAS DONE WITH SHARPENED MAPS. IN THE SODIUM BINDING SITE BETWEEN RESIDUES ALA38 AND THR330 THERE IS ADDITIONAL DENSITY THAT HAS NOT BEEN MODELLED.
Rfactor
Num. reflection
% reflection
Rfree
0.3126
2204
9.9 %
Rwork
0.2732
-
-
obs
0.2773
22378
90.16 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.262 e/Å3
Displacement parameters
Biso mean: 242 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-32.6384 Å2
0 Å2
0 Å2
2-
-
-32.6384 Å2
-0 Å2
3-
-
-
53.8407 Å2
Refinement step
Cycle: LAST / Resolution: 3.8→33.388 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3585
0
0
0
3585
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.115
3925
X-RAY DIFFRACTION
f_angle_d
1.037
5034
X-RAY DIFFRACTION
f_dihedral_angle_d
17.584
1246
X-RAY DIFFRACTION
f_chiral_restr
0.061
595
X-RAY DIFFRACTION
f_plane_restr
0.005
616
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.8002-3.8828
0.4652
146
0.4346
1181
X-RAY DIFFRACTION
83
3.8828-3.9729
0.4165
105
0.4539
1129
X-RAY DIFFRACTION
82
3.9729-4.0721
0.4568
133
0.43
1143
X-RAY DIFFRACTION
82
4.0721-4.182
0.4069
139
0.4186
1196
X-RAY DIFFRACTION
84
4.182-4.3048
0.3962
152
0.3706
1169
X-RAY DIFFRACTION
86
4.3048-4.4435
0.4021
121
0.3376
1250
X-RAY DIFFRACTION
90
4.4435-4.6019
0.3736
126
0.3353
1286
X-RAY DIFFRACTION
89
4.6019-4.7857
0.3667
118
0.3081
1264
X-RAY DIFFRACTION
90
4.7857-5.0028
0.3289
140
0.2712
1290
X-RAY DIFFRACTION
92
5.0028-5.2656
0.3981
157
0.2835
1266
X-RAY DIFFRACTION
92
5.2656-5.594
0.3391
116
0.2729
1324
X-RAY DIFFRACTION
93
5.594-6.0236
0.2801
118
0.249
1360
X-RAY DIFFRACTION
95
6.0236-6.6256
0.3442
144
0.2541
1332
X-RAY DIFFRACTION
96
6.6256-7.5745
0.2552
162
0.2019
1368
X-RAY DIFFRACTION
98
7.5745-9.5065
0.1783
158
0.1609
1376
X-RAY DIFFRACTION
99
9.5065-33.3897
0.3247
169
0.2721
1240
X-RAY DIFFRACTION
91
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
0.2125
2.0747
-2.0731
1.7964
-3.0455
-0.3158
0.3908
-0.7069
0.3853
0.5107
-0.0458
-0.7946
0.9144
0.0541
-0.0003
2.7533
0.0812
-0.0036
2.6944
0.075
2.3804
35.47
-34.3017
17.1569
2
0.7263
-0.1078
-1.1739
0.7752
3.7417
1.2087
0.3652
0.2368
-1.3189
0.3941
-0.576
-0.7743
0.5555
-0.123
0.0007
2.408
-0.0568
-0.0466
2.2207
0.7151
2.7606
48.449
-47.8788
8.6233
3
1.175
-1.6615
0.203
0.6913
0.6407
-0.5274
-1.4742
-1.4717
3.3383
0.8823
0.7287
-2.2437
-0.8632
-2.339
-0.1628
2.3232
-0.3102
0.6871
2.5866
0.6105
2.3349
34.1023
-54.2278
20.2136
4
-0.7126
-0.1316
0.4455
0.7481
-0.2851
-1.9919
0.3549
-1.1772
-1.3407
-0.6649
1.081
-1.6591
-0.0632
0.0359
0.0003
2.8109
0.3703
0.4154
2.8006
0.0608
3.1057
62.6161
-32.9468
1.7312
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
RESSEQ100:160ORRESSEQ295:358
2
X-RAY DIFFRACTION
2
RESSEQ8:99ORRESSEQ192:294
3
X-RAY DIFFRACTION
3
RESSEQ161:191
4
X-RAY DIFFRACTION
4
RESSEQ359:470
+
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