5QUA
Crystal Structure of swapped human Nck SH3.1 domain, 1.5A, C2221
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1 M Bis-Tris/HCl pH 6.5, 2 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.56 | 21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.6 | α = 90 |
b = 85.19 | β = 90 |
c = 56.19 | 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 | PSI PILATUS 6M | 2019-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.00005 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.5 | 35.32 | 99.7 | 0.026 | 0.029 | 1 | 21.87 | 6.4 | 20939 | 47.855 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.5 | 1.54 | 97.5 | 0.14 | 6.505 |
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 | inhouse model | 1.51 | 35.32 | 14743 | 706 | 75.84 | 0.2014 | 0.2001 | 0.2275 | RANDOM | 45.595 |
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] | |
0.17 | -0.57 | 0.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.722 |
r_dihedral_angle_4_deg | 25.163 |
r_dihedral_angle_3_deg | 15.698 |
r_dihedral_angle_1_deg | 7.913 |
r_angle_refined_deg | 1.723 |
r_angle_other_deg | 1.312 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 953 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |