1OD8
Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E0X | PDB ENTRY 1E0X |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 20 MG/ML PROTEIN, 16% PEG 5K MME, 100 MM IMIDAZOLE, PH 7.5, 5% ISOPROPANOL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.814 | ¦Á = 90 |
b = 45.878 | ¦Â = 90 |
c = 85.737 | ¦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 | TORROIDAL MIRROR | 2002-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.05 | 20 | 98 | 0.062 | 26.4 | 4.7 | 121638 |
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 | 1.05 | 1.09 | 86.4 | 0.441 | 2.3 | 2.05 |
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 1E0X | 1.05 | 19.8 | 112969 | 5945 | 97.9 | 0.104 | 0.103 | 0.126 | RANDOM | 8.12 |
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] | |
0.11 | 0.04 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.229 |
r_scangle_it | 4.558 |
r_scbond_it | 3.441 |
r_mcangle_it | 2.81 |
r_mcbond_it | 2.03 |
r_angle_refined_deg | 1.689 |
r_angle_other_deg | 0.85 |
r_metal_ion_refined | 0.614 |
r_nbd_other | 0.455 |
r_symmetry_vdw_other | 0.427 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2324 |
Nucleic Acid Atoms | |
Solvent Atoms | 629 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |