4RGG
Structure of the lactococcal phage 1358 receptor binding protein in complex with GlcNAc-1P
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4L92 | PDB ENTRY 4L92 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.2 | 293 | 20% w/v polyethyleneglycol 1000, 100 mM sodium/potassium phosphate buffer, pH 6.2, 200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.39 | 71.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 165.91 | α = 90 |
b = 165.91 | β = 90 |
c = 165.91 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 | 2014-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR |
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 | 2.15 | 48 | 99.9 | 0.089 | 20.5 | 12.3 | 81936 | 49 |
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 | 2.15 | 2.21 | 99.9 | 0.81 | 2.43 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MIR | THROUGHOUT | PDB ENTRY 4L92 | 2.15 | 47.89 | 38297 | 78636 | 3914 | 100 | 0.181 | 0.18 | 0.204 | RANDOM | 45.25 |
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 |
r_long_range_B_other | 9.341 |
r_long_range_B_refined | 9.318 |
r_scangle_other | 6.74 |
r_mcangle_other | 5.458 |
r_mcangle_it | 5.109 |
r_scbond_it | 4.375 |
r_scbond_other | 4.313 |
r_mcbond_it | 3.444 |
r_mcbond_other | 3.444 |
r_angle_refined_deg | 1.893 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6056 |
Nucleic Acid Atoms | |
Solvent Atoms | 502 |
Heterogen Atoms | 38 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |