Joint X-ray/neutron structure of PKG II CNB-B domain in complex with 8-pCPT-cGMP
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 5BV6 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277 | 30% MPD, 20 mM SrCl2, 100 mM NaOAc pH 4.6 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.19 | 43.96 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 43.65 | α = 90 |
b = 51.3 | β = 90 |
c = 68.2 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2015-11-01 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | COLLIMATORS | 2015-11-26 | L | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | | |
2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.8-4.0 | ILL | LADI III |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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1 | 2 | 10 | 97.3 | 0.064 | | | | | | 12.5 | 3.3 | | 10492 | | | |
2 | 2.2 | 40 | 74.7 | 0.141 | | | | | | 7.5 | 3.6 | | 5966 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2 | 2.06 | | 0.535 | | | | | | 2.8 | 3.2 | |
2 | 2.2 | 2.32 | | 0.19 | | | | | | 4.5 | 2.4 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 10 | | 2 | | 10401 | 487 | 96 | | | 0.199 | 0.245 | RANDOM | 38.16 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 40 | | 2 | | 5949 | 287 | 72.6 | | | 0.232 | 0.288 | RANDOM | 38.16 |
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] |
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| | | | | |
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Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1214 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 40 |
Software
Software |
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Software Name | Purpose |
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nCNS | refinement |
LAUEGEN | data reduction |
LSCALE | data scaling |
PHASER | phasing |