2UWB
Crystal structure of the Nasturtium seedling mutant xyloglucanase isoform NXG1-delta-YNIIG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2UWA | PDB ENTRY 2UWA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 1.4 M SODIUM ACETATE AND 100 MM SODIUM-CACODYLATE BUFFER AT PH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.62 | 73.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 153.894 | α = 90 |
b = 153.894 | β = 90 |
c = 83.819 | γ = 120 |
Symmetry | |
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Space Group | P 6 |
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 | 2006-12-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 45 | 100 | 0.11 | 18.7 | 10.8 | 76393 | 0.5 |
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 | 2.11 | 100 | 0.49 | 4.7 | 10.8 |
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 2UWA | 2 | 40 | 72537 | 3844 | 100 | 0.194 | 0.193 | 0.213 | RANDOM | 22.14 |
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] | |
-0.63 | -0.31 | -0.63 | 0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.898 |
r_dihedral_angle_4_deg | 16.036 |
r_dihedral_angle_3_deg | 14.32 |
r_dihedral_angle_1_deg | 7.512 |
r_scangle_it | 2.952 |
r_scbond_it | 2.067 |
r_angle_refined_deg | 1.533 |
r_mcangle_it | 1.347 |
r_mcbond_it | 1.123 |
r_angle_other_deg | 0.875 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4312 |
Nucleic Acid Atoms | |
Solvent Atoms | 235 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |