6RS7
X-ray crystal structure of LsAA9B (deglycosylated form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3EJA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | 16%(w/v) MPD (racemic) 16%(w/v) PEG 1000 16%(w/v) PEG 3350 20 mM of Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic). 30 mM of each of NaNO3; Na2HPO4; (NH4)2SO4 100 mM Imidazole/MES 0.1 M (pH6.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.08 | α = 90 |
b = 72.99 | β = 90 |
c = 79.06 | γ = 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 | MARMOSAIC 225 mm CCD | Collimating mirror , double-crystal monochromator (DCM), focusing mirror | 2014-02-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 1.0000 | MAX II | I911-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 1.6 | 20 | 98.5 | 0.084 | 0.998 | 14.39 | 5.81 | 27139 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.7 | 91.7 | 0.82 | 0.766 | 1.94 | 3.59 |
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 | 3EJA | 1.6 | 20 | 25753 | 1386 | 98.51 | 0.15476 | 0.15171 | 0.21142 | RANDOM | 18.437 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.23 | 1.69 | -1.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.544 |
r_dihedral_angle_4_deg | 23.654 |
r_sphericity_bonded | 15.84 |
r_dihedral_angle_3_deg | 11.707 |
r_dihedral_angle_1_deg | 6.019 |
r_rigid_bond_restr | 5.376 |
r_long_range_B_refined | 3.102 |
r_long_range_B_other | 3.102 |
r_scangle_other | 2.151 |
r_scbond_it | 1.699 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1645 |
Nucleic Acid Atoms | |
Solvent Atoms | 240 |
Heterogen Atoms | 89 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MxCuBE | data collection |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Coot | model building |