4RK7
Crystal structure of LacI family transcriptional regulator CCPA from Weissella paramesenteroides, Target EFI-512926, with bound sucrose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4RK6 | PDB ENTRY 4RK6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.641 M malonic acid, 0.088 M ammonium citrate tribasic, 0.042 M succinic acid, 0.105 M DL-malic acid, 0.14 M sodium acetate, 0.175 M sodium formate, 0.056 M ammonium tartrate dibasic, cryoprotectant = reservoir + 100 mM sucrose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.694 | α = 90 |
b = 102.694 | β = 90 |
c = 127.699 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | ADSC QUANTUM 315r | mirrors | 2014-09-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
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 | 1.8 | 50 | 100 | 0.068 | 0.068 | 33 | 12 | 63693 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.8 | 1.83 | 99.8 | 2.4 | 11.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4RK6 | 1.8 | 50 | 61741 | 1880 | 99.94 | 0.16215 | 0.16113 | 0.19467 | RANDOM | 39.639 |
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] | |
-0.16 | -0.16 | 0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.9 |
r_scbond_it | 16.413 |
r_scbond_other | 16.413 |
r_scangle_other | 15.7 |
r_long_range_B_other | 15.501 |
r_long_range_B_refined | 15.323 |
r_dihedral_angle_4_deg | 15.064 |
r_dihedral_angle_3_deg | 13.206 |
r_mcangle_it | 8.481 |
r_mcangle_other | 8.48 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4242 |
Nucleic Acid Atoms | |
Solvent Atoms | 385 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHASER | phasing |
ARP/wARP | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |