system development / cell development / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function
Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 1997 / Details: MIRRORS
Radiation
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.997 Å / Relative weight: 1
Reflection
Resolution: 2.7→20 Å / Num. obs: 8927 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 93.5 Å2 / Rsym value: 0.041 / Net I/σ(I): 18.9
Reflection shell
Resolution: 2.7→2.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.286 / % possible all: 88.5
Reflection
*PLUS
Num. measured all: 33776 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 88.5 % / Rmerge(I) obs: 0.286
-
Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
3.8
modelbuilding
X-PLOR
3.8
refinement
X-PLOR
3.8
phasing
Refinement
Method to determine structure: MIR / Resolution: 2.7→10 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: AT EARLY STAGES, PROGRAM REFMAC WAS USED. TO ACCOUNT FOR AVERAGED BASE PAIRS (D6-D10, E26-E30), TWO STRUCTURES CONTAINING DIFFERENT DNA STRANDS (CHAIN E AND D) WERE REFINED INDIVIDUALLY. AT ...Details: AT EARLY STAGES, PROGRAM REFMAC WAS USED. TO ACCOUNT FOR AVERAGED BASE PAIRS (D6-D10, E26-E30), TWO STRUCTURES CONTAINING DIFFERENT DNA STRANDS (CHAIN E AND D) WERE REFINED INDIVIDUALLY. AT A FINAL STAGE, BOTH DNA STRANDS WERE INCLUDED IN THE MODEL AND GIVEN HALF OCCUPANCY. CYS 126 AND CYS 131 ARE IN CLOSE PROXIMITY AND THE ELECTRON DENSITY WOULD ALSO ALLOW MODELING OF A DISULPHIDE BRIDGE. THIS MIGHT INDICATE PARTIAL OXIDATION. LOOP 81-84 IS BADLY ORDERED. DURING REFINEMENT, IT HAS BEEN GIVEN AN OCCUPANCY OF 0.5. LYS 222 IS THE LAST RESIDUE IN THE MODEL. THE QUALITY OF ITS ELECTRON DENSITY IS POOR AND DID NOT ALLOW UNAMBIGUOUS MODELING. THE C-TERMINAL DIMERIZATION DOMAIN OF THE REL HOMOLOGY REGION OF GAMBIF1 IS PRESENT IN THE USED CONSTRUCT AND THE CRYSTALS. HOWEVER, IT IS DISORDERED AND COULD NOT BE INCLUDED IN THE MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.288
404
4.7 %
RANDOM
Rwork
0.219
-
-
-
obs
0.219
8575
84.1 %
-
Displacement parameters
Biso mean: 52.8 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.84 Å2
-
-
2-
-
-3.84 Å2
-
3-
-
-
7.68 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1377
609
0
36
2022
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.011
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.7
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
3.6
2.5
X-RAY DIFFRACTION
x_mcangle_it
5.6
2.5
X-RAY DIFFRACTION
x_scbond_it
6.4
3.5
X-RAY DIFFRACTION
x_scangle_it
8.7
3.5
LS refinement shell
Resolution: 2.7→2.82 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
Rfactor
Num. reflection
% reflection
Rfree
0.426
51
5 %
Rwork
0.436
1013
-
obs
-
-
88.5 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PARHCSDX.PRO
TOPHCSDX.PRO
X-RAY DIFFRACTION
2
DNA-RNA.PARAM
TOPH19.PEP
X-RAY DIFFRACTION
3
PARAM19.SOL
DNA-RNA.TOP
X-RAY DIFFRACTION
4
TOPH19.SOL
+
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