4BJ8
Zebavidin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | THE PROTEIN SOLUTION (1.6 MG/ML; 50 MM TRIS-HCL. PH 7) WAS MIXED WITH BIOTIN SOLUTION (1 MG/ML; 5 MM TRIS, PH 8.8, 8 MM CHES, PH 9.5) IN 10:1 V/V RATIO BEFORE CRYSTALLIZATION. SITTING DROPS WITH 300 NL OF PROTEIN-LIGAND SOLUTION AND 150 NL OF WELL SOLUTION (0.18 M MAGNESIUM CHLORIDE, 0.09 M BIS TRIS, PH 5.5, 23% W/V PEG 3350) WERE USED. 30% V/V GLYCEROL IN WELL SOLUTION WAS ADDED TO THE DROP BEFORE FREEZING IN LIQUID NITROGEN. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 182.24 | α = 90 |
b = 196.84 | β = 90 |
c = 52.59 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | ADSC QUANTUM 4 | 2012-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 2.4 | 25 | 100 | 0.12 | 14 | 8.2 | 74935 | -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 | 2.4 | 2.5 | 99 | 0.61 | 3 | 8.3 |
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 1WBI | 2.4 | 24.58 | 71194 | 3741 | 99.81 | 0.19546 | 0.19173 | 0.26596 | RANDOM | 27.233 |
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] | |
1.44 | -0.78 | -0.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.86 |
r_dihedral_angle_3_deg | 17.426 |
r_dihedral_angle_4_deg | 17.132 |
r_dihedral_angle_1_deg | 7.176 |
r_angle_refined_deg | 1.749 |
r_angle_other_deg | 0.863 |
r_chiral_restr | 0.096 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14505 |
Nucleic Acid Atoms | |
Solvent Atoms | 503 |
Heterogen Atoms | 262 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |