Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
TWO RESIDUES ADDED AT N-TERMINUS OF CHAIN A DERIVED FROM PRESCISSION CLEAVAGE SITE. TWO RESIDUES AT ...TWO RESIDUES ADDED AT N-TERMINUS OF CHAIN A DERIVED FROM PRESCISSION CLEAVAGE SITE. TWO RESIDUES AT N-TERMINUS OF CHAIN B ADDED FROM TEV CLEAVAGE SEQUENCE
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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal grow
pH: 6.5 Details: 100 MM MES PH 6.0, 0.22 M SODIUM MALONATE, 18 % PEG 8000
Monochromator: DOUBLE CRYSTAL FIXED-EXIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0077 Å / Relative weight: 1
Reflection
Resolution: 1.9→79 Å / Num. obs: 74599 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.3
Reflection shell
Resolution: 1.9→2 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.4 / % possible all: 95.4
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: INITIAL MODEL GENERATED FROM A GOLD DERIVATIVE SOLVED IN SPACE GROUP C 2 Resolution: 1.902→88 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 21.54 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.21
3763
5 %
Rwork
0.185
-
-
obs
0.1863
74599
98.74 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.139 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Biso mean: 30.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-4.3242 Å2
0 Å2
0 Å2
2-
-
8.2976 Å2
0 Å2
3-
-
-
-3.9734 Å2
Refinement step
Cycle: LAST / Resolution: 1.902→88 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4985
0
67
654
5706
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
5221
X-RAY DIFFRACTION
f_angle_d
1.035
7118
X-RAY DIFFRACTION
f_dihedral_angle_d
14.461
1962
X-RAY DIFFRACTION
f_chiral_restr
0.064
858
X-RAY DIFFRACTION
f_plane_restr
0.006
914
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.902-1.9261
0.4003
128
0.3187
2614
X-RAY DIFFRACTION
98
1.9261-1.9514
0.2876
123
0.2993
2551
X-RAY DIFFRACTION
98
1.9514-1.9782
0.3151
149
0.2684
2559
X-RAY DIFFRACTION
98
1.9782-2.0064
0.289
136
0.2409
2529
X-RAY DIFFRACTION
98
2.0064-2.0364
0.2916
121
0.2215
2615
X-RAY DIFFRACTION
98
2.0364-2.0682
0.2228
155
0.2163
2600
X-RAY DIFFRACTION
98
2.0682-2.1021
0.2492
147
0.2092
2554
X-RAY DIFFRACTION
98
2.1021-2.1384
0.2749
128
0.2021
2619
X-RAY DIFFRACTION
98
2.1384-2.1772
0.257
145
0.196
2581
X-RAY DIFFRACTION
98
2.1772-2.2191
0.1818
134
0.1881
2605
X-RAY DIFFRACTION
99
2.2191-2.2644
0.1933
114
0.1814
2617
X-RAY DIFFRACTION
98
2.2644-2.3137
0.2195
138
0.1844
2597
X-RAY DIFFRACTION
99
2.3137-2.3675
0.2163
140
0.1807
2597
X-RAY DIFFRACTION
99
2.3675-2.4267
0.2249
135
0.1817
2627
X-RAY DIFFRACTION
99
2.4267-2.4923
0.2235
144
0.1838
2600
X-RAY DIFFRACTION
99
2.4923-2.5657
0.2095
144
0.1917
2608
X-RAY DIFFRACTION
99
2.5657-2.6485
0.2587
148
0.1922
2615
X-RAY DIFFRACTION
99
2.6485-2.7431
0.2121
118
0.1952
2669
X-RAY DIFFRACTION
99
2.7431-2.853
0.2195
140
0.1883
2634
X-RAY DIFFRACTION
99
2.853-2.9828
0.2047
140
0.1893
2614
X-RAY DIFFRACTION
99
2.9828-3.1401
0.2131
130
0.1887
2668
X-RAY DIFFRACTION
99
3.1401-3.3368
0.2037
153
0.1876
2638
X-RAY DIFFRACTION
100
3.3368-3.5945
0.1919
150
0.1688
2654
X-RAY DIFFRACTION
99
3.5945-3.9562
0.1796
147
0.1534
2678
X-RAY DIFFRACTION
100
3.9562-4.5287
0.1505
166
0.1386
2663
X-RAY DIFFRACTION
99
4.5287-5.7055
0.1775
136
0.1632
2712
X-RAY DIFFRACTION
99
5.7055-88.0943
0.2179
154
0.2007
2818
X-RAY DIFFRACTION
99
+
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