1YH3
Crystal structure of human CD38 extracellular domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 297 | MES, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.839 | α = 108.27 |
b = 51.491 | β = 90.47 |
c = 66.439 | γ = 97.29 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC QUANTUM 4 | 2004-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | 0.916 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 30 | 97.9 | 41065 | 40203 | 1 | 1 |
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 | 1.9 | 1.93 | 94.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.91 | 10 | 39418 | 37426 | 1992 | 98.06 | 0.19174 | 0.19174 | 0.18849 | 0.25336 | RANDOM | 28.562 |
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] | |
-2.17 | 0.66 | 1.21 | 1.15 | 2.56 | 2.81 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 7.334 |
r_scangle_it | 6.297 |
r_scbond_it | 4.2 |
r_mcangle_it | 2.659 |
r_angle_refined_deg | 2.264 |
r_mcbond_it | 1.539 |
r_symmetry_vdw_refined | 0.409 |
r_nbd_refined | 0.263 |
r_xyhbond_nbd_refined | 0.206 |
r_symmetry_hbond_refined | 0.191 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3986 |
Nucleic Acid Atoms | |
Solvent Atoms | 324 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |