2PAF
Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EFA | pdb entry 1EFA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 281 | 1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.541 | α = 90 |
b = 77.541 | β = 90 |
c = 212.456 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | IMAGE PLATE | MAR scanner 300 mm plate | Osmic Blue Max mirrors | 2006-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 3.5 | 20 | 99.1 | 0.166 | 0.166 | 5.9 | 4.9 | 8745 | 8685 | -3 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
3.5 | 3.62 | 99.5 | 0.336 | 0.336 | 3.5 | 5 |
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 1EFA | 3.5 | 19.81 | 8745 | 8252 | 413 | 99.09 | 0.19856 | 0.19537 | 0.26516 | RANDOM | 28.204 |
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] | |
-0.02 | -0.02 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.519 |
r_dihedral_angle_3_deg | 22.382 |
r_dihedral_angle_4_deg | 17.799 |
r_dihedral_angle_1_deg | 8.195 |
r_scangle_it | 3.312 |
r_scbond_it | 1.929 |
r_angle_refined_deg | 1.805 |
r_mcangle_it | 1.364 |
r_mcbond_it | 0.964 |
r_nbtor_refined | 0.326 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4028 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |