6R64
N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in complex with C5mCGG target sequence
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6GHC | PDB ENTRY 6GHC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 294 | NEco in the crystallization buffer (20 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 1 mM EDTA, 2 mM DTT) was concentrated to 8.7 mg/ml and mixed in the 1:1.2 ratio with 10-mer TCAC5mCGGTTC oligonucleotide, annealed to its complementary GAAC5mCGTGA strand. Crystals were grown by mixing 1.8 ul of the protein-DNA mixture with 2.2 ul of the condition F1 of the PACT premier crystal screen (MDL) (0.2 M NaF, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350). Crystals were cryo-protected by the addition of 25% glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
8.29 | 85.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.432 | α = 90 |
b = 112.432 | β = 90 |
c = 155.457 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 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 | PIXEL | DECTRIS PILATUS 6M | 2018-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91840 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | CC (Half) | 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 | 2.64 | 45.55 | 99.8 | 0.223 | 0.23 | 0.997 | 12.52 | 16 | 17671 | 50.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.64 | 2.8 | 99.2 | 1.463 | 1.509 | 0.764 | 1.97 | 16.7 |
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 6GHC | 2.64 | 45.55 | 16786 | 884 | 99.82 | 0.19237 | 0.19052 | 0.22921 | RANDOM | 53.738 |
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] | |
-1.73 | -0.87 | -1.73 | 5.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.592 |
r_dihedral_angle_4_deg | 18.898 |
r_dihedral_angle_3_deg | 12.424 |
r_dihedral_angle_1_deg | 5.38 |
r_long_range_B_refined | 4.943 |
r_long_range_B_other | 4.915 |
r_scangle_other | 3.299 |
r_mcangle_it | 2.258 |
r_mcangle_other | 2.257 |
r_scbond_it | 1.894 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2320 |
Nucleic Acid Atoms | 812 |
Solvent Atoms | 141 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
ARP/wARP | model building |