Joint X-ray/neutron structure of PKGIbeta in complex with cGMP
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 1.4 M Na3Citrate, pH 6.5 and 0.2 M NaI solutions, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.84 | 33.08 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 48.746 | α = 90 |
| b = 48.746 | β = 90 |
| c = 104.861 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 41 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS IV++ | OSMIC VARIMAX | 2013-04-24 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | cylindrical neutron image plate | SET OF COLLIMATORS | 2013-05-10 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | | 2.8-4.0 | | LADI-III |
Data Collection
| Overall |
|---|
| 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 |
|---|
| 1 | 1.76 | 40 | 98.7 | 0.044 | | | | | | 35 | 7.3 | | 13053 | | | |
| 2 | 2.2 | 40 | 82.7 | 0.07 | | | | | | 13.8 | 4 | | 5642 | | | |
| Highest Resolution Shell |
|---|
| 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) |
|---|
| 1.76 | 1.82 | | 0.547 | | | | | | 2.8 | 6.6 | |
| 2.2 | 2.32 | | 0.198 | | | | | | 4.9 | 2.9 | |
Refinement
| Statistics |
|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 40 | | 2.5 | 5851 | 5552 | 256 | 80.3 | 0.277 | 0.277 | 0.277 | | 0.318 | | random | |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| x_dihedral_angle_d | 17.3 |
| x_improper_angle_d | 8.75 |
| x_angle_deg | 1.7 |
| x_bond_d | 0.12 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1003 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 111 |
| Heterogen Atoms | 24 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| Maatel | data collection |
| HKL-3000 | data reduction |
| LAUEGEN | data reduction |
| HKL-3000 | data scaling |
| LSCALE | data scaling |
| CNS | phasing |
