5UN2
Crystal Structure of Mouse Cadherin-23 EC19-21 with non-syndromic deafness (DFNB12) associated mutation R2029W
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5TFK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 277 | 0.1 M HEPES pH 7.3 0.1 M CaCl2 27% PEG 400 5% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.64 | 73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 189.475 | α = 90 |
b = 73.908 | β = 96.62 |
c = 49.375 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 200K | 2017-01-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-003 | 1.542 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.96 | 50 | 91.5 | 0.164 | 0.187 | 0.087 | 7.863 | 3.8 | 14294 | 36.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.96 | 3.01 | 95.3 | 0.554 | 0.631 | 0.294 | 1.97 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5TFK | 2.96 | 50 | 12402 | 668 | 91.42 | 0.19818 | 0.19618 | 0.23582 | RANDOM | 48.334 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.72 | 2.12 | 5.61 | -6.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.78 |
r_dihedral_angle_4_deg | 18.701 |
r_dihedral_angle_3_deg | 14.839 |
r_dihedral_angle_1_deg | 7.152 |
r_long_range_B_refined | 2.445 |
r_long_range_B_other | 2.375 |
r_angle_refined_deg | 1.44 |
r_mcangle_it | 0.952 |
r_mcangle_other | 0.952 |
r_angle_other_deg | 0.927 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2563 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |