4JCY
Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR operator complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) PEG3350, 10 mM spermidine, protein dimer/DNA molar ratio 1:1, protein concentration 4.6 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.34 | α = 90 |
b = 62.34 | β = 90 |
c = 158.08 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 120 | PIXEL | PSI PILATUS 6M | 2012-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9795 | Diamond | I02 |
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 | 1.8 | 53.99 | 99.5 | 0.059 | 12.8 | 4.2 | 32091 | 30476 | 2 |
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 | 1.8 | 1.9 | 99.8 | 0.551 | 2.6 | 4 |
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 3LFP | 1.8 | 53.99 | 32091 | 30476 | 1614 | 99.9 | 0.14788 | 0.14712 | 0.1626 | RANDOM | 30.616 |
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] | |
0.41 | 0.41 | -0.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.751 |
r_dihedral_angle_4_deg | 12.664 |
r_dihedral_angle_3_deg | 11.329 |
r_dihedral_angle_1_deg | 4.041 |
r_angle_refined_deg | 0.952 |
r_chiral_restr | 0.066 |
r_gen_planes_refined | 0.005 |
r_bond_refined_d | 0.004 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1494 |
Nucleic Acid Atoms | 855 |
Solvent Atoms | 402 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |