DNA-BINDINGPROTEININHIBITORID-2 / CLASS D BASIC HELIX-LOOP-HELIX PROTEIN 26 / CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 26 / BHLHB26 / ...CLASS D BASIC HELIX-LOOP-HELIX PROTEIN 26 / CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 26 / BHLHB26 / INHIBITOR OF DNA BINDING 2
Mass: 10844.563 Da / Num. of mol.: 2 / Fragment: HELIX-LOOP-HELIX DOMAIN, RESIDUES 1-82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST-565 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02363
Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence details
FIRST RESIDUE IN SEQUENCE AFTER TEV CLEAVAGE IS A GLYCINE. ID2 SEQUENCE NUMBERING STARTS FROM ...FIRST RESIDUE IN SEQUENCE AFTER TEV CLEAVAGE IS A GLYCINE. ID2 SEQUENCE NUMBERING STARTS FROM SECOND RESIDUE, METHIONINE. RESIDUE 83 ONWARDS CONTAINS THE C-TERMINAL STABILIZER POLYPEPTIDE.
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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal grow
pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M MES PH6.5, 2.0 M POTASSIUM ACETATE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0809 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. obs: 10569 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 41.98 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.6
Reflection shell
Resolution: 2.1→2.18 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.2 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
PHENIX
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: INTERNAL SELENOMETHIONINE-SUBSTITUTED ID2 STRUCTURE AT 3.0A Resolution: 2.103→44.706 Å / SU ML: 0.23 / σ(F): 0.65 / Phase error: 27.31 / Stereochemistry target values: ML Details: RESIDUES 1-29 ARE MISSING IN CHAIN A. RESIDUES 1-34 ARE MISSING IN CHAIN B.
Rfactor
Num. reflection
% reflection
Rfree
0.2497
987
9.8 %
Rwork
0.2246
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-
obs
0.2271
10026
95.2 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parameters
Biso mean: 54.4 Å2
Refinement step
Cycle: LAST / Resolution: 2.103→44.706 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
870
0
6
24
900
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
888
X-RAY DIFFRACTION
f_angle_d
1.071
1198
X-RAY DIFFRACTION
f_dihedral_angle_d
13.029
346
X-RAY DIFFRACTION
f_chiral_restr
0.059
141
X-RAY DIFFRACTION
f_plane_restr
0.004
149
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.1031-2.2139
0.3049
129
0.2513
1147
X-RAY DIFFRACTION
88
2.2139-2.3526
0.3124
136
0.2351
1228
X-RAY DIFFRACTION
91
2.3526-2.5343
0.3081
133
0.2357
1229
X-RAY DIFFRACTION
94
2.5343-2.7893
0.2775
140
0.2585
1300
X-RAY DIFFRACTION
97
2.7893-3.1928
0.3268
148
0.2613
1335
X-RAY DIFFRACTION
98
3.1928-4.0222
0.2479
148
0.2096
1356
X-RAY DIFFRACTION
100
4.0222-44.716
0.1968
153
0.2091
1444
X-RAY DIFFRACTION
99
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