2BF6
Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SLL | PDB ENTRY 1SLL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 20 % PEG 3350, 0.2M POTASSIUM NITRATE, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.981 | α = 90 |
b = 69.413 | β = 90 |
c = 72.694 | 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 | ADSC CCD | MIRRORS | 2004-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 0.97 | 57 | 91 | 0.1 | 11.8 | 3.8 | 290992 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 0.97 | 1.03 | 87 | 0.19 | 5 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB ENTRY 1SLL | 0.97 | 57 | 264777 | 13089 | 91.8 | 0.1133 | 0.1134 | 0.1331 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
11 | 3285.2 | 4037.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.11 |
s_zero_chiral_vol | 0.103 |
s_approx_iso_adps | 0.092 |
s_anti_bump_dis_restr | 0.081 |
s_from_restr_planes | 0.0348 |
s_similar_adp_cmpnt | 0.032 |
s_angle_d | 0.031 |
s_bond_d | 0.016 |
s_rigid_bond_adp_cmpnt | 0.006 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3524 |
Nucleic Acid Atoms | |
Solvent Atoms | 485 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |