6KXL
Crystal structure of the catalytic domain of Chitiniphilus shinanonensis chitinase ChiL (CsChiL) complexed with N,N'-diacetylchitobiose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6KST |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293.15 | 0.2 M sodium malonate, 29% w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.982 | α = 90 |
b = 82.502 | β = 90 |
c = 131.818 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 95 | CCD | ADSC QUANTUM 210r | Focusing mirror | 2014-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.000 | Photon Factory | AR-NW12A |
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 | 1.35 | 50 | 95.8 | 0.076 | 0.083 | 0.031 | 11.4 | 6.7 | 157981 | 12 |
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 | 1.35 | 1.4 | 82.5 | 0.442 | 0.486 | 0.197 | 0.928 | 4 | 5.7 |
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 | 6KST | 1.35 | 31.21 | 149276 | 7893 | 95.21 | 0.1196 | 0.1181 | 0.1477 | RANDOM | 15.029 |
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] | |
-0.76 | 1.25 | -0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.687 |
r_dihedral_angle_4_deg | 13.135 |
r_dihedral_angle_3_deg | 11.06 |
r_dihedral_angle_1_deg | 6.538 |
r_rigid_bond_restr | 3.248 |
r_angle_other_deg | 1.661 |
r_angle_refined_deg | 1.392 |
r_chiral_restr | 0.069 |
r_bond_other_d | 0.018 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5816 |
Nucleic Acid Atoms | |
Solvent Atoms | 1212 |
Heterogen Atoms | 209 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |