3ESM
Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 3.5 | 294 | 100mM citric acid pH 3.5, 2.0M ammonium sulfate, Vapor diffusion, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.582 | α = 90 |
b = 67.582 | β = 90 |
c = 62.571 | γ = 120 |
Symmetry | |
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Space Group | P 32 1 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2008-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97958 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.65 | 29.735 | 100 | 0.081 | 0.081 | 20.2 | 18.7 | 19837 | 19837 | 24 |
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) | ||||||||||
1.65 | 1.74 | 99.9 | 0.531 | 0.531 | 3.5 | 18.7 | 2885 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.65 | 20 | 19819 | 19809 | 1029 | 99.95 | 0.232 | 0.23 | 0.262 | RANDOM | 33.09 |
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] | |
0.54 | 0.27 | 0.54 | -0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.713 |
r_dihedral_angle_4_deg | 20.562 |
r_dihedral_angle_3_deg | 11.488 |
r_dihedral_angle_1_deg | 5.645 |
r_scangle_it | 4.218 |
r_scbond_it | 2.525 |
r_mcangle_it | 1.743 |
r_angle_refined_deg | 1.564 |
r_mcbond_it | 0.985 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1039 |
Nucleic Acid Atoms | |
Solvent Atoms | 111 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
MOSFLM | data reduction |
SHELXCD | phasing |
SHELXE | model building |