5KNH
CRYSTAL STRUCTURE OF DARPIN 6G9 IN COMPLEX WITH CYNO IL-13
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3L5X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 293 | 11% PEG 3350, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.41 | α = 90 |
b = 78.49 | β = 90 |
c = 119.44 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | MIRRORS | 2012-02-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.9999 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.6 | 30 | 99.6 | 0.065 | 17.1 | 6.4 | 32998 | -3 | 25.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.6 | 1.64 | 96.4 | 0.542 | 3.7 | 6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3L5X | 1.6 | 15 | 31810 | 1040 | 96.4 | 0.16881 | 0.16793 | 0.19577 | RANDOM | 23.1 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.64 | -1.57 | 0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.405 |
r_scbond_it | 33.144 |
r_scangle_it | 31.921 |
r_dihedral_angle_4_deg | 10.997 |
r_dihedral_angle_3_deg | 10.572 |
r_dihedral_angle_1_deg | 4.679 |
r_mcangle_it | 4.469 |
r_mcbond_it | 2.699 |
r_angle_refined_deg | 1.156 |
r_chiral_restr | 0.077 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1908 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
REFMAC | refinement |