6MLY
Bifunctional GH43-CE Bacteroides eggerthii, BACEGG_01304
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZXL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.5 | 294 | 0.2M AmSO4, 0.1M MES pH 6.5, 30% PEG 5k; streak seeding to produce larger crystals |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.08 | 60.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 254.734 | α = 90 |
b = 93.31 | β = 123.38 |
c = 214.039 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | RAYONIX MX300-HS | 2018-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.979 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.7 | 50 | 99.8 | 0.161 | 0.192 | 0.103 | 4.8 | 3.4 | 113694 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.7 | 2.75 | 99.9 | 1.105 | 1.338 | 0.746 | 0.466 | 3.1 |
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 | 3ZXL | 2.7 | 48.16 | 107971 | 5719 | 98.78 | 0.2222 | 0.2198 | 0.2686 | RANDOM | 62.463 |
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] | |
-1.05 | 3.78 | -7.08 | 1.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 73.485 |
r_dihedral_angle_2_deg | 32.05 |
r_sphericity_bonded | 23.149 |
r_dihedral_angle_4_deg | 18.217 |
r_dihedral_angle_3_deg | 15.835 |
r_dihedral_angle_1_deg | 7.63 |
r_rigid_bond_restr | 2.298 |
r_angle_refined_deg | 0.96 |
r_angle_other_deg | 0.714 |
r_chiral_restr | 0.044 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23692 |
Nucleic Acid Atoms | |
Solvent Atoms | 396 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MrBUMP | phasing |