2YBU
Crystal structure of human acidic chitinase in complex with bisdionin F
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LG2 | PDB ENTRY 1LG2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.4 | 75% SATURATED NACL, 0.1 M HEPES PH 7.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 62 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 144.781 | ¦Á = 90 |
b = 149.194 | ¦Â = 90 |
c = 151.278 | ¦Ã = 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 | 100 | CCD | ADSC CCD | 2006-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 2.25 | 20 | 99.6 | 0.1 | 14.8 | 4.1 | 154470 | 31.9 |
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 | 2.25 | 2.33 | 99.8 | 0.58 | 2.7 | 4.1 |
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 | PDB ENTRY 1LG2 | 2.25 | 19.97 | 152900 | 1544 | 99.62 | 0.17343 | 0.17296 | 0.21916 | RANDOM | 28.703 |
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] | |
0.51 | -1.1 | 0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.255 |
r_dihedral_angle_4_deg | 19.648 |
r_dihedral_angle_3_deg | 16.45 |
r_dihedral_angle_1_deg | 6.063 |
r_scangle_it | 5.099 |
r_scbond_it | 3.375 |
r_mcangle_it | 2.095 |
r_angle_refined_deg | 1.89 |
r_mcbond_it | 1.121 |
r_chiral_restr | 0.144 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17856 |
Nucleic Acid Atoms | |
Solvent Atoms | 1119 |
Heterogen Atoms | 372 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |