2Q2H
Crystal structure of the protein secretion chaperone CsaA from Agrobacterium tumefaciens with a genetically fused phage-display derived peptide substrate at the N-terminus.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GD7 | pdb entry 1gd7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 292 | 30% PEG 4000, 0.4 M ammonium acetate, 0.1 M sodium citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.528 | α = 90 |
b = 60.528 | β = 90 |
c = 115.247 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | IMAGE PLATE | RIGAKU RAXIS IV | VariMax Cu HF | 2006-10-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.54 |
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 | 1.65 | 23.86 | 89.4 | 0.039 | 30 | 5.71 | 25681 | 25681 | 5 | 5 |
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 | 1.65 | 1.71 | 49.7 | 0.162 | 8.6 | 4.47 | 1427 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1gd7 | 1.65 | 23.86 | 25680 | 25680 | 1301 | 89.38 | 0.161 | 0.161 | 0.16 | 0.173 | RANDOM | 8.236 |
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] | |
-0.01 | -0.01 | -0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.742 |
r_dihedral_angle_4_deg | 18.172 |
r_dihedral_angle_3_deg | 12.237 |
r_dihedral_angle_1_deg | 6.282 |
r_scangle_it | 1.663 |
r_angle_refined_deg | 1.183 |
r_scbond_it | 1.155 |
r_mcangle_it | 0.693 |
r_mcbond_it | 0.446 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1696 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
CrystalClear | data reduction |
PHASER | phasing |