4L1G
Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase from Bacillus cereus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1W1B | PDB ENTRY 1W1B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 291 | 15% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.657 | α = 90 |
b = 92.657 | β = 90 |
c = 242.947 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | MAR CCD 165 mm | monochromators | 2009-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.817 | EMBL/DESY, HAMBURG | BW7A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.336 | 80 | 100 | 45861 | 0.5 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.336 | 2.3868 | 99.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | PDB ENTRY 1W1B | 2.336 | 30.639 | 1.33 | 45310 | 45341 | 2282 | 98.86 | 0.1814 | 0.1792 | 0.223 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 10.776 |
f_angle_d | 0.758 |
f_chiral_restr | 0.055 |
f_plane_restr | 0.004 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6842 |
Nucleic Acid Atoms | |
Solvent Atoms | 769 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |