6NJI
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.14 | 289 | 5.0MG/ML VCID7620 + 0.5MM T-049 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214023) AGAINST OPTIMIZATION MATRIX BASED ON CONDITION MORPHEUS C8, 47.47%V/V OF 2X MORPHEUS-PPT4 (FINAL = 11.8% W/V PEG1,000 , 11.8% W/V PEG3,350 , 11.8% W/V MPD), 0.03M NPS (SODIUM NITRATE, DISODIUM HYDROGEN PHOSPHATE, AMMONIUM SULFATE), 0.1M HEPES PH 7.14, CRYO-PROTECTED - DIRECT (ZQV4-6); TRAY ID 236552B5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.66 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 124.04 | ¦Á = 90 |
b = 85.66 | ¦Â = 110.41 |
c = 83.45 | ¦Ã = 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 | CCD | MARMOSAIC 225 mm CCD | 2012-08-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.45 | 50 | 97.9 | 0.046 | 20.27 | 3.3 | 29617 | -3 | 56.07 |
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 | 2.45 | 2.51 | 99 | 0.504 | 2.5 | 3.3 |
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 | 2.45 | 42.87 | 29616 | 1504 | 99 | 0.187 | 0.184 | 0.23 | RANDOM | 50.86 |
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] | |
0.8 | 0.06 | 1.3 | -1.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.73 |
r_dihedral_angle_4_deg | 23.778 |
r_dihedral_angle_3_deg | 14.995 |
r_dihedral_angle_1_deg | 5.21 |
r_angle_refined_deg | 1.534 |
r_angle_other_deg | 0.987 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5210 |
Nucleic Acid Atoms | |
Solvent Atoms | 69 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |