4KYW
Restriction endonuclease DPNI in complex with two DNA molecules
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ESJ | PDB ENTRY 4ESJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | 160 mM CALCIUM ACETATE, 80 mM SODIUM CACODYLATE PH 6.5, 14.4% W/V PEG 8000, 20% V/V GLYCEROL, 10 mM SPERMIDINE., VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.28 | 62.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.7 | α = 90 |
b = 101.05 | β = 90 |
c = 114.85 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | PSI PILATUS 6M | 2012-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 1.23953 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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 | 2.35 | 50 | 99.7 | 0.049 | 0.049 | 20.51 | 6.37 | 23502 | 23502 |
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) | ||||||||||
1 | 2.35 | 2.41 | 99.9 | 0.44 | 0.44 | 4.14 | 6.68 | 1720 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4ESJ | 2.35 | 46.23 | 23477 | 23477 | 1204 | 99.72 | 0.20216 | 0.20216 | 0.20125 | 0.21904 | RANDOM | 43.385 |
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] | |
-0.77 | -0.42 | 1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.887 |
r_dihedral_angle_4_deg | 19.589 |
r_dihedral_angle_3_deg | 15.495 |
r_dihedral_angle_1_deg | 6.217 |
r_angle_other_deg | 3.804 |
r_scangle_it | 2.848 |
r_scbond_it | 1.794 |
r_angle_refined_deg | 1.34 |
r_mcangle_it | 1.282 |
r_mcbond_it | 0.675 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2096 |
Nucleic Acid Atoms | 812 |
Solvent Atoms | 94 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
ARP/wARP | model building |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |