5A71
Open and closed conformations and protonation states of Candida antarctica Lipase B: atomic resolution native
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TCA | PDB ENTRY 1TCA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 293 | CANDIDA ANTARCTICA LIPASE B (CALB) WAS PURCHASED BY HAMPTON RESEARCH AND CRYSTALLIZED WITHOUT FURTHER PURIFICATION. CRYSTALLIZATION TRIALS WERE PERFORMED AT 293 K USING THE HANGING-DROP METHOD USING A QUIAGEN EASYXTAL 15-WELL PLATE. 1 UL OF A 15 MG/ML CALB SOLUTION IN 20MM NA(CH3COO) PH = 4.8 WAS DILUTED WITH 1 UL OF THE PRECIPITANT SOLUTION, MADE OF 200MM NA(CH3COO) PH = 4.8, 20% (W/V) PEG4000, AND 10-13% (V/V) 2-PROPANOL. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION AGAINST 500 ML OF THE PRECIPITANT SOLUTION. PROTEIN CRYSTALS OF NATIVE CALB APPEARED WITHIN ONE WEEK AND GREW TO A SIZE OF 0.2 X 0.4 X 0.5 MM3 IN THREE WEEKS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.67 | α = 88.74 |
b = 48.94 | β = 97.15 |
c = 71.61 | γ = 108.44 |
Symmetry | |
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Space Group | P 1 |
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 | PIXEL | DECTRIS PILATUS 6M | KB MIRRORS | 2013-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 0.91 | 71.04 | 94.5 | 0.11 | 13.65 | 17.2 | 343684 | 1.5 |
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 | 0.91 | 0.93 | 77.4 | 0.57 | 1.59 | 3.5 |
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 1TCA | 0.91 | 71.04 | 326301 | 17383 | 94.48 | 0.11255 | 0.1115 | 0.13197 | RANDOM | 11.793 |
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] | |
-0.04 | -0.23 | -0.1 | 0.4 | 0.16 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 35.794 |
r_dihedral_angle_2_deg | 33.317 |
r_dihedral_angle_4_deg | 20.037 |
r_dihedral_angle_3_deg | 11.303 |
r_sphericity_bonded | 11.239 |
r_rigid_bond_restr | 6.779 |
r_dihedral_angle_1_deg | 6.583 |
r_angle_refined_deg | 2.257 |
r_scbond_it | 2.177 |
r_mcangle_it | 1.565 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4632 |
Nucleic Acid Atoms | |
Solvent Atoms | 1019 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |