6NJJ
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 298 | 8.8MG/ML VCID7620 + 0.5MM BPN- 014770 (EBSI4045) IN A PROTEIN SOLUTION CONTAINING 10MM HEPES PH 7.5, 100MM NACL, 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214057) AGAINST OPTIMIZATION SCREEN TET_MPC8_JCH7 (OPT SCREEN BASED ON MORPHEUS C8 AND JCSG H7); 6.25% W/V PEG1,000, 20.91% W/V PEG3350, 6.25% W/V MPD, 0.2M AMMONIUM SULFATE, 0.1MM BIS- TRIS PH 6.3, CRYO-PROTECTED - 20% ETHYLENE GLYCOL, CRYSTAL TRACKING ID 247599D11 (WEV9-9), PH 6.30, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.65 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 81.33 | ¦Á = 90 |
b = 82.05 | ¦Â = 110.01 |
c = 116.35 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 315r | 2013-09-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 0.9765 | ALS | 5.0.3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.3 | 50 | 99.7 | 0.086 | 0.998 | 13.68 | 3.8 | 64038 | -3 | 39.87 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.36 | 99.8 | 0.558 | 0.859 | 2.6 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.3 | 45.49 | 64022 | 3241 | 99.8 | 0.17 | 0.167 | 0.214 | RANDOM | 31.06 |
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] | |
-0.05 | -2.45 | 1.59 | 0.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.131 |
r_dihedral_angle_4_deg | 15.934 |
r_dihedral_angle_3_deg | 13.576 |
r_dihedral_angle_1_deg | 5.154 |
r_mcangle_it | 3.847 |
r_mcbond_it | 2.627 |
r_mcbond_other | 2.627 |
r_angle_refined_deg | 1.578 |
r_angle_other_deg | 1.226 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10543 |
Nucleic Acid Atoms | |
Solvent Atoms | 505 |
Heterogen Atoms | 174 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |