4F46
Crystal structure of wild type human CD38 in complex with NAADP and ADPRP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 298 | 0.1M sodium acetate pH 4.0, 15% PEG 10K, 0.2M ammonium acetate, 3% isopropanol, vapor diffusion, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.848 | α = 110.35 |
b = 53.683 | β = 91.42 |
c = 63.38 | γ = 94.53 |
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 | MX225 | 2009-09-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.97623 | SSRF | BL17U |
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 | 1.69 | 100 | 95 | 0.079 | 17.2 | 7.1 | 53940 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 1.76 | 68.5 | 0.213 | 4.3 | 3904 |
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 | 1YH3 | 1.69 | 50 | 53915 | 2718 | 94.14 | 0.1679 | 0.1664 | 0.1948 | RANDOM | 31.0308 |
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] | |
-1.12 | -0.06 | 0.08 | 0.4 | 0.45 | 1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.896 |
r_dihedral_angle_4_deg | 13.669 |
r_dihedral_angle_3_deg | 12.033 |
r_dihedral_angle_1_deg | 5.57 |
r_angle_refined_deg | 1.209 |
r_angle_other_deg | 0.867 |
r_chiral_restr | 0.069 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4058 |
Nucleic Acid Atoms | |
Solvent Atoms | 392 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |