2HWV
Crystal structure of an essential response regulator DNA binding domain, VicRc in Enterococcus faecalis, a member of the YycF subfamily.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OPC | PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ |
experimental model | PDB | 1YS6 | PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ |
experimental model | PDB | 1P2F | PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ |
experimental model | PDB | 1GXQ | PDB ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 291 | 1.8M ammonium sulphate, 0.1M sodium citrate, 3% dimethyl sulfoxide, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.71 | 28.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.235 | α = 90 |
b = 36.235 | β = 90 |
c = 73.935 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic Confocal Max-Flux | 2006-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.9 | 36.226 | 99.5 | 0.053 | 0.053 | 11.2 | 6.2 | 7524 | 7524 | 27.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 2 | 98.9 | 0.347 | 0.347 | 4.8 | 5.7 | 1083 |
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 ENTRIES 1OPC, 1YS6, 1P2F, 1GXQ | 1.9 | 12 | 7545 | 7134 | 345 | 99.57 | 0.18114 | 0.17865 | 0.23619 | RANDOM | 19.596 |
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] | |
0.77 | 0.77 | -1.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.973 |
r_dihedral_angle_4_deg | 19.526 |
r_dihedral_angle_3_deg | 18.347 |
r_dihedral_angle_1_deg | 6.899 |
r_scangle_it | 3.674 |
r_scbond_it | 2.36 |
r_angle_refined_deg | 1.497 |
r_mcangle_it | 1.407 |
r_mcbond_it | 0.864 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 844 |
Nucleic Acid Atoms | |
Solvent Atoms | 52 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
PHASER | phasing |