4ID6
Crystal Structure of Staphylococcal nuclease mutant V23I/I72L
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EY0 | PBD ENTRY 1EY0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.3 | α = 90 |
b = 48.3 | β = 90 |
c = 63.9 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | 298 | CCD | RIGAKU SATURN 92 | mirrors | 2012-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
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 | 1.898 | 21.62 | 98.1 | 0.048 | 10.2 | 2.3 | 26211 | 11415 | 50 | 3 |
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 | 1.898 | 1.97 | 98.1 | 0.048 | 1.3 |
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 | PBD ENTRY 1EY0 | 1.898 | 21.6 | 11415 | 10865 | 543 | 97.86 | 0.19012 | 0.18761 | 0.2415 | RANDOM | 40.175 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.792 |
r_dihedral_angle_3_deg | 19.197 |
r_dihedral_angle_4_deg | 18.608 |
r_scangle_it | 6.609 |
r_dihedral_angle_1_deg | 6.232 |
r_scbond_it | 4.003 |
r_mcangle_it | 2.641 |
r_angle_refined_deg | 2.067 |
r_mcbond_it | 1.44 |
r_chiral_restr | 0.143 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1092 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
CCP4 | model building |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
CCP4 | phasing |