6EZS
Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase from Vibrio harveyi in complex with N-acetylglucosamine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6EZR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 4.5 | 293 | 0.1 M sodium acetate pH 4.6, 1.4 M sodium malonate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.69 | 66.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.25 | α = 90 |
b = 129.63 | β = 114.36 |
c = 100 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | PIXEL | DECTRIS PILATUS 6M | 2012-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.97889 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | CC (Half) | 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 | 2.5 | 48.02 | 99.4 | 0.12 | 0.99 | 9.71 | 4.7 | 72950 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.56 | 99.9 | 0.53 | 0.85 | 3.17 | 4.53 |
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 | 6ezr | 2.5 | 48.02 | 69303 | 3648 | 99.56 | 0.2024 | 0.2001 | 0.2476 | RANDOM | 35.901 |
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] | |
0.43 | 0.03 | -1.19 | 0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.809 |
r_dihedral_angle_4_deg | 20.219 |
r_dihedral_angle_3_deg | 17.017 |
r_dihedral_angle_1_deg | 5.692 |
r_angle_refined_deg | 1.284 |
r_angle_other_deg | 1.086 |
r_chiral_restr | 0.067 |
r_bond_refined_d | 0.009 |
r_bond_other_d | 0.006 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10286 |
Nucleic Acid Atoms | |
Solvent Atoms | 885 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
PHASER | phasing |
Coot | model building |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |