4WUZ
Crystal structure of lambda exonuclease in complex with DNA and Ca2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.5 | 295 | 23.4% PEG 3350, 0.3M sodium acetate, 0.1 M Tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.038 | α = 90 |
b = 80.038 | β = 90 |
c = 241.596 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | AREA DETECTOR | CUSTOM-MADE | 2010-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 2.38 | 69.34 | 99.9 | 0.187 | 6.5 | 11.5 | 33237 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.38 | 2.51 | 100 | 0.644 | 3.2 | 11.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 2.38 | 69.34 | 33237 | 1754 | 99.97 | 0.23894 | 0.23471 | 0.31934 | RANDOM | 30.323 |
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] | |
-0.21 | -0.1 | -0.21 | 0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.018 |
r_dihedral_angle_4_deg | 17.827 |
r_dihedral_angle_3_deg | 17.612 |
r_dihedral_angle_1_deg | 6.641 |
r_scangle_it | 3.784 |
r_scbond_it | 2.444 |
r_angle_refined_deg | 1.751 |
r_mcangle_it | 1.673 |
r_mcbond_it | 0.893 |
r_chiral_restr | 0.114 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5366 |
Nucleic Acid Atoms | 533 |
Solvent Atoms | 236 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOLREP | phasing |
MOSFLM | data reduction |
SCALA | data scaling |