2Q1F
Crystal structure of chondroitin sulfate lyase abc from bacteroides thetaiotaomicron wal2926
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 282 | 17% PEG 3350, 0.2M ammonium sulfate, 100 mM HEPES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K, pH 6.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.44 | 64.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 223.362 | α = 90 |
b = 223.362 | β = 90 |
c = 112.639 | 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 300 mm CCD | DOUBLE-CRYSTAL FIXED-EXIT SI- 111 MONOCHROMATOR (E/E~10-4) AND A PLANAR PALLADIUM-COATED SILICON MIRROR | 2006-05-26 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.85 | 50 | 94.7 | 0.063 | 0.05 | 14.6 | 3.1 | 71079 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.85 | 2.92 | 56.7 | 0.4 | 0.326 | 1.6 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.85 | 50 | 67482 | 3599 | 94.8 | 0.222 | 0.22 | 0.262 | RANDOM | 59.33 |
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] | |
-1.88 | -0.94 | -1.88 | 2.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.854 |
r_dihedral_angle_3_deg | 17.472 |
r_dihedral_angle_4_deg | 15.287 |
r_dihedral_angle_1_deg | 5.167 |
r_scangle_it | 1.864 |
r_mcangle_it | 1.214 |
r_scbond_it | 1.195 |
r_angle_refined_deg | 1.007 |
r_mcbond_it | 0.826 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15824 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
SHARP | phasing |