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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
3VBC
Crystal Structure of iL-17 receptor B SEFIR domain
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
pH
6
Temperature
293.0
Details
0.2 M NaAc, pH 5.0, 1.6 M Ammonium citrate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 54.97
α = 90
b = 65.8
β = 90
c = 89.64
γ = 90
Symmetry
Space Group
I 2 2 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315
--
2011-07-20
Diffraction Radiation
Monochromator
Protocol
GRAPHITE
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 19-ID
--
APS
19-ID
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
1.8
50
99.4
0.1
0.1
--
6.6
--
15902
--
2.3
21.0
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
SAD
1.8
32.9
--
1.34
--
15387
771
99.6
--
0.183
0.181
0.223
--
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
1.8
1.9128
--
150
2351
0.3247
0.3956
--
98.0
X Ray Diffraction
1.9128
2.0605
--
119
2416
0.232
0.2759
--
100.0
X Ray Diffraction
2.0605
2.2678
--
122
2398
0.1824
0.2276
--
100.0
X Ray Diffraction
2.2678
2.5958
--
113
2449
0.1668
0.1844
--
100.0
X Ray Diffraction
2.5958
3.27
--
135
2453
0.16
0.2099
--
100.0
X Ray Diffraction
3.27
32.904
--
132
2549
0.1664
0.2
--
100.0
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
isotropic
Anisotropic B[1][1]
-0.6921
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
2.01
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-1.3179
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.071
f_angle_d
1.003
f_plane_restr
0.004
f_bond_d
0.007
f_dihedral_angle_d
17.699
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
1086
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
73
Software
Software
Software Name
Purpose
HKL-3000
data collection
HKL-3000
phasing
PHENIX
refinement version: (phenix.refine: 1.6_289)
HKL-3000
data reduction
HKL-3000
data scaling