4MFG
2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH 7.5, 2% MPD, 20% (w/v) PEG 3350; Cryo: paratone., VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.089 | α = 90 |
b = 127.089 | β = 90 |
c = 76.732 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | Beryllium lenses | 2011-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 30 | 99.9 | 0.107 | 29.5 | 9.7 | 47926 | 47926 | -3 | 19.1 |
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 | 2.03 | 100 | 0.61 | 3.8 | 9.5 | 2398 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1XHD | 2 | 29.36 | 45299 | 45299 | 2416 | 99.87 | 0.21439 | 0.21439 | 0.21158 | 0.26663 | RANDOM | 42.179 |
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] | |
0.89 | 0.45 | 0.89 | -2.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.44 |
r_dihedral_angle_4_deg | 12.229 |
r_dihedral_angle_3_deg | 11.971 |
r_long_range_B_refined | 6.838 |
r_long_range_B_other | 6.628 |
r_dihedral_angle_1_deg | 3.762 |
r_scangle_other | 3.322 |
r_scbond_it | 2.412 |
r_scbond_other | 2.397 |
r_mcangle_it | 2.199 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5152 |
Nucleic Acid Atoms | |
Solvent Atoms | 406 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |