3RU5
Silver Metallated Hen Egg White Lysozyme at 1.35 A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KAM | PDB ENTRY 3KAM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 293 | 5 mM silver(I) 3-hydroxybutyrate, 3% (w/v) sodium nitrate, 25% (v/v) ethylene glycol, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.99 | 38.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.798 | α = 90 |
b = 77.798 | β = 90 |
c = 37.629 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | CCD | APEX II CCD | 2011-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER IMUS MICROFOCUS | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.35 | 25.55 | 99.7 | 32.84 | 18.08 | 25991 | 25935 |
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 3KAM | 1.35 | 25.55 | 24429 | 1303 | 99.25 | 0.19348 | 0.19237 | 0.21451 | RANDOM | 15.317 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.01 |
r_dihedral_angle_4_deg | 19.991 |
r_dihedral_angle_3_deg | 12.804 |
r_dihedral_angle_1_deg | 5.553 |
r_sphericity_free | 4.001 |
r_sphericity_bonded | 2.818 |
r_scangle_it | 2.782 |
r_scbond_it | 2.393 |
r_rigid_bond_restr | 1.923 |
r_mcangle_it | 1.419 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
APEX | data collection |
PHASER | phasing |
REFMAC | refinement |
SAINT | data reduction |
APEX | data reduction |