4NW7
PDE4 catalytic domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 289 | VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM T-028-1 (COMPOUND #7) AGAINST JCSG_B9 OPTIMIZATION SCREEN 0.1M SODIUM CITRATE TRIBASIC / CITRIC ACID, PH 5.5, 19.45% W/V PEG 6,000, CRYO 20% ETHYLENE GLYCOL AND 0.1MM T-028-1, CRYSTAL TRACKING ID 232699H5, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.58 | α = 90 |
b = 98.58 | β = 90 |
c = 47.57 | γ = 90 |
Symmetry | |
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Space Group | P 42 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2012-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07809 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.15 | 49.29 | 99.3 | 0.091 | 12.68 | 4 | 25192 | 25012 | -3 | 32.32 |
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 | 2.15 | 2.21 | 99.3 | 0.505 | 3 | 4.1 | 1848 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.15 | 49.29 | 25192 | 25006 | 1274 | 0.158 | 0.155 | 0.207 | RANDOM | 28.71 |
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] | |
-0.36 | -0.36 | 0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.042 |
r_dihedral_angle_4_deg | 17.612 |
r_dihedral_angle_3_deg | 14.03 |
r_dihedral_angle_1_deg | 5.294 |
r_mcangle_it | 3.052 |
r_mcbond_it | 2.085 |
r_mcbond_other | 2.085 |
r_angle_refined_deg | 1.595 |
r_angle_other_deg | 0.953 |
r_chiral_restr | 0.093 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2710 |
Nucleic Acid Atoms | |
Solvent Atoms | 193 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |