6K6V
Crystal structure of barley exohydrolaseI W434A mutant in complex with methyl 6-thio-beta-gentiobioside
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3WLI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.5 | 64.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.524 | α = 90 |
b = 100.524 | β = 90 |
c = 182.076 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 QUANTUM 210r | COLLIMATING MIRROR | 2012-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
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 | 1.98 | 88 | 97 | 0.082 | 38.7 | 29 | 62175 |
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 | 1.98 | 2.03 | 0.082 |
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 | 3WLI | 1.98 | 29.35 | 62175 | 3324 | 99.81 | 0.1451 | 0.1438 | 0.1714 | RANDOM | 28.737 |
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] | |
1.1 | 1.1 | -2.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.293 |
r_dihedral_angle_4_deg | 17.282 |
r_dihedral_angle_3_deg | 13.288 |
r_dihedral_angle_1_deg | 6.411 |
r_angle_refined_deg | 1.445 |
r_angle_other_deg | 1.083 |
r_chiral_restr | 0.082 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4587 |
Nucleic Acid Atoms | |
Solvent Atoms | 704 |
Heterogen Atoms | 119 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |