5WJ8
Crystal Structure of Human Cadherin-23 EC13-14
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5VH2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | 0.1 M NaOAc pH 4.5 0.2 M CaCl2 30 (v/v) isopropanol 20% (v/v) glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.48 | 64.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.712 | α = 90 |
b = 74.712 | β = 90 |
c = 213.507 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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-F | 2017-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9792 | APS | 24-ID-C |
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 | 1.86 | 71.17 | 94.4 | 0.076 | 26.8 | 10.2 | 30738 |
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 | 1.86 | 1.89 | 83.3 | 0.538 | 2 | 7.1 |
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 | 5VH2 | 1.86 | 71.17 | 27574 | 1422 | 94.56 | 0.21843 | 0.2169 | 0.24828 | RANDOM | 45.936 |
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] | |
1.66 | 0.83 | 1.66 | -5.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.26 |
r_dihedral_angle_4_deg | 16.959 |
r_dihedral_angle_3_deg | 11.421 |
r_long_range_B_refined | 6.008 |
r_dihedral_angle_1_deg | 5.935 |
r_long_range_B_other | 5.887 |
r_scangle_other | 1.609 |
r_angle_refined_deg | 1.5 |
r_mcangle_it | 1.454 |
r_mcangle_other | 1.453 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1610 |
Nucleic Acid Atoms | |
Solvent Atoms | 133 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |