3GI1
Crystal Structure of the laminin-binding protein Lbp of Streptococcus pyogenes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TOA | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
experimental model | PDB | 1K0F | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
experimental model | PDB | 1PQ4 | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
experimental model | PDB | 1XVL | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
experimental model | PDB | 2O1E | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
experimental model | PDB | 3HH8 | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 291 | 0.7ul of 37 mg/ml Lbp in PBS, pH7.4 + 0.002% Na-azide + 0.7ul of 30% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.624 | α = 90 |
b = 92.163 | β = 106.27 |
c = 70.614 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR345DTB | osmic mirrors | 2007-08-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.4 | 27.984 | 99.9 | 0.098 | 0.098 | 6.861 | 7.3 | 20587 | 20587 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.4 | 2.53 | 100 | 0.597 | 0.597 | 1.2 | 7.2 | 3004 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1TOA, 1K0F, 1PQ4, 1XVL, 2O1E, 3HH8 | 2.45 | 27.982 | 1.93 | 20569 | 1947 | 99.97 | 0.19 | 0.186 | 0.251 | 39.498 |
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] | |
7.381 | 7.209 | -5.336 | -2.045 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.163 |
f_angle_d | 1.56 |
f_chiral_restr | 0.103 |
f_bond_d | 0.015 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3902 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |