2HUB
Structure of Hen Egg-White Lysozyme Determined from crystals grown in pH 7.5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Microbatch, Douglas Instrument robot | 7.5 | 293 | 0.1 M HEPES-Na pH 7.5, 0.8M Potassium Sodium Tartrate tetrahydrate, Microbatch, Douglas Instrument robot, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.861 | α = 90 |
b = 76.861 | β = 90 |
c = 35.867 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | Mirrors | 2005-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.9737 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.201 | 54.31 | 98.2 | 0.054 | 0.054 | 16.8 | 6.2 | 33587 | 33587 | -3 | 10.95 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||||
1.201 | 1.22 | 74.3 | 0.475 | 0.419 | 2.1 | 2.7 | 1242 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MAD | THROUGHOUT | In-house structure | 1.201 | 54.31 | -3 | 33538 | 33538 | 1688 | 98.38 | 0.138 | 0.138 | 0.137 | 0.173 | RANDOM | 11.052 |
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] | |
-1.12 | -1.12 | 2.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.808 |
r_dihedral_angle_4_deg | 23.904 |
r_sphericity_free | 14.246 |
r_dihedral_angle_3_deg | 11.511 |
r_sphericity_bonded | 8.756 |
r_scangle_it | 6.77 |
r_dihedral_angle_1_deg | 5.976 |
r_scbond_it | 5.48 |
r_mcangle_it | 4.055 |
r_mcbond_other | 3.411 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1069 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |