3PYK
Human Carbonic Anhydrase II as Host for Pianostool Complexes Bearing a Sulfonamide Anchor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CBA | PDB entry 2cba |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | 3 uL protein solution (20 mg/mL lyophilized hCAII in 50 mM Tris-sulfate, 1 mM methyl mercuric acetate) and 5 uL precipitating buffer (2.6 M ammonium sulfate, 50 mM Tris-sulfate were mixed and equilibrated against 500 uL precipitating buffer. Single crystals were transferred into a cross-linking buffer, which was prepared from 10 uL precipitating buffer and 5 uL glutaraldehyde solution (0.8 % glutaraldehyde, 4 M ammonium sulfate, 50 mM Tris-sulfate) and equilibrated for 18 h. Cross-linked crystals were transferred into soaking buffer (9 uL precipitating buffer, 0.5 uL 60 mM {(6-benzene)Ru(bispy 3)Cl}+ in DMSO) and equilibrated for 54 h, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.099 | α = 90 |
b = 41.493 | β = 104.33 |
c = 72.382 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 225 mm CCD | 2011-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OTHER | 1.0 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.3 | 30.6 | 96.9 | 59007 | 2 | 2 |
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 | 1.3 | 1.334 | 91.2 | 0.309 | 2.8 | 2.7 |
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 2cba | 1.3 | 30.6 | 59007 | 2984 | 98.74 | 0.12947 | 0.12756 | 0.16471 | RANDOM | 12.373 |
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 | -0.28 | 0.15 | -0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.962 |
r_dihedral_angle_4_deg | 17.319 |
r_dihedral_angle_3_deg | 12.195 |
r_scangle_it | 8.349 |
r_dihedral_angle_1_deg | 6.622 |
r_scbond_it | 6.395 |
r_mcangle_it | 4.386 |
r_mcbond_it | 3.195 |
r_rigid_bond_restr | 2.895 |
r_angle_refined_deg | 1.454 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2058 |
Nucleic Acid Atoms | |
Solvent Atoms | 420 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |