1W25
Response regulator PleD in complex with c-diGMP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.2 | CRYSTALS WERE OBTAINED AT ROOM TEMPERATURE BY HANGING DROP VAPOUR DIFFUSION. FOR THIS, PLED AT A NOMINAL CONCENTRATION OF 10 MG/ML IN 20 MM TRIS-HCL (PH 8.0), 100 MM NACL, 1 MM DTT, 2 MM MGCL2 AND 0.8 MM C-DIGMP6 WAS MIXED WITH THE RESERVOIR (1.0 M GLYCINE PH 9.2, 2 % DIOXANE, 14.5 % POLYETHYLENE GLYCOL 20K) AT A RATIO 1 TO 1. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.9 | 69 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 135.87 | ¦Á = 90 |
b = 135.87 | ¦Â = 90 |
c = 169.247 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 42 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 | MARRESEARCH | 2003-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA |
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 | 2.7 | 60.86 | 99.3 | 0.08 | 16.42 | 5.7 | 43706 | -3.7 |
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 | 2.7 | 2.72 | 98.7 | 0.36 | 2.96 | 5.48 |
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 | MAD | THROUGHOUT | 2.7 | 50 | 41469 | 2202 | 98.9 | 0.212 | 0.21 | 0.239 | RANDOM | 25.61 |
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] | |
-0.07 | -0.07 | 0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.956 |
r_dihedral_angle_4_deg | 16.945 |
r_dihedral_angle_3_deg | 16.4 |
r_dihedral_angle_1_deg | 5.586 |
r_scangle_it | 3.706 |
r_scbond_it | 2.416 |
r_mcangle_it | 1.307 |
r_angle_refined_deg | 1.211 |
r_mcbond_it | 1.129 |
r_angle_other_deg | 0.773 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6962 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms | 233 |
Software
Software | |
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Software Name | Purpose |
DM | model building |
TRUNCATE | data scaling |
SHELXD | phasing |
SHARP | phasing |
SOLOMON | phasing |
DM | phasing |
REFMAC | refinement |