4B1A
Crystal structure of lysozyme with Keggin molecule
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | 2-10% (M/V) NACL AND 0.1 M ACETATE BUFFER PH 4.5 (THE PROTEIN:WELL SOLUTION RATIO IN THE DROP WAS 1:1 WITH THE FINAL DROP VOLUME OF 4 MICROLITER USING A PROTEIN STOCK CONCENTRATION OF AROUND 50 MG/ML. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.91 | 35.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.96 | α = 90 |
b = 77.96 | β = 90 |
c = 36.41 | 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 | 160 | CCD | ADSC QUANTUM 210 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 1.67 | 30.38 | 99.6 | 0.02 | 29.7 | 13.5 | 13544 | -1 |
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 | 1.67 | 1.76 | 100 | 0.1 | 6.4 | 13.4 |
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 193L | 1.67 | 30.38 | 12793 | 667 | 99.48 | 0.21501 | 0.21249 | 0.26664 | RANDOM | 22.674 |
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] | |
-1.47 | -1.47 | 2.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.837 |
r_dihedral_angle_4_deg | 20.704 |
r_dihedral_angle_3_deg | 14.229 |
r_dihedral_angle_1_deg | 7.299 |
r_scangle_it | 4.522 |
r_scbond_it | 2.999 |
r_mcangle_it | 1.891 |
r_angle_refined_deg | 1.84 |
r_mcbond_it | 1.194 |
r_angle_other_deg | 1.184 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 987 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PHASER | phasing |