4NVP
Structure of the cyclic nucleotide-binding domain of HCN4 channel complexed with 7-CH-cAMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | HCN4 521-723 (10 mg mL-1) and 7-CH-cAMP 0.5mM were mixed in a 2:1 ratio with 100 mM TrisCl pH 8.0, 20 % PEG4000 (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.01 | α = 90 |
b = 96.01 | β = 90 |
c = 50.17 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
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 | bending magnet; bent collimating mirror and toroid | 2013-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97372 | ESRF | BM14 |
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 | 2.5 | 50.17 | 100 | 0.08 | 16.4 | 8.1 | 8568 | 8568 | 5 | 33.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.5 | 2.64 | 99.9 | 0.45 | 4.3 | 7.7 | 1215 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 3U11_A | 2.5 | 44.47 | 8148 | 8141 | 406 | 99.92 | 0.20117 | 0.19799 | 0.27031 | RANDOM | 42.441 |
Temperature Factor Modeling | ||||||
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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 | -0.05 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.176 |
r_dihedral_angle_3_deg | 19.842 |
r_dihedral_angle_4_deg | 13.757 |
r_long_range_B_refined | 8.003 |
r_long_range_B_other | 8.001 |
r_dihedral_angle_1_deg | 6.32 |
r_scangle_other | 5.814 |
r_mcangle_other | 4.421 |
r_mcangle_it | 4.42 |
r_scbond_it | 3.6 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1661 |
Nucleic Acid Atoms | |
Solvent Atoms | 37 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
AMoRE | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |