4BBO
Crystal structure of core-bradavidin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Y32 | PDB ENTRY 2Y32 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | ONE MICROLITER OF THE PROTEIN SOLUTION (LESS THAN 1 MG PER ML AND IN 50 MM SODIUM ACETATE, 100 MM NACL, PH 4) WAS CRYSTALLIZED BY ADDING ONE MICROLITER OF THE WELL SOLUTION (0.1 M HEPES PH 7.4, 0.8 M K,NA TARTRATE).HANGING DROPS AND VAPOUR DIFFUSION METHOD WAS USED AT RT. BEFORE CRYSTALLIZATION, 25 MICROLITERS OF THE PROTEIN SAMPLE WAS INCUBATED WITH 1 MICRO LITER OF BIOTIN SOLUTION (1 MG PER ML AND IN 5 MM TRIS PH 8.8, 8 MM CHES PH 9.5) FOR 3.5 HOURS AT 37 DEGREES OF CELCIUS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.946 | α = 90 |
b = 78.647 | β = 90 |
c = 100.12 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2005-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I711 | MAX II | I711 |
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 | 1.6 | 25 | 100 | 0.09 | 18 | 9.6 | 52798 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.6 | 1.7 | 100 | 0.55 | 4 | 9.6 |
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 2Y32 | 1.6 | 61.9 | 50108 | 2690 | 99.95 | 0.14843 | 0.14685 | 0.17863 | RANDOM | 14.577 |
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] | |
1.11 | -0.78 | -0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.969 |
r_dihedral_angle_3_deg | 10.92 |
r_dihedral_angle_1_deg | 6.071 |
r_scangle_it | 2.715 |
r_scbond_it | 1.838 |
r_angle_refined_deg | 1.457 |
r_mcangle_it | 1.224 |
r_mcbond_it | 0.626 |
r_chiral_restr | 0.099 |
r_bond_refined_d | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3313 |
Nucleic Acid Atoms | |
Solvent Atoms | 368 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |