3D9Y
Crystal Structure of Profilin from Schizosaccharomyces pombe
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 1.3 M Na Malonate; 0.2 M Hepes pH 7.0; 0.5% JeffamineED2001 [O O'-BIS (2-aminopropyl) polyethylene glycol 1900] from Hampton Research], VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.533 | α = 90 |
b = 84.021 | β = 93.73 |
c = 40.42 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 273 | IMAGE PLATE | MAR scanner 345 mm plate | 2006-10-02 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | CCD | MARRESEARCH | 2007-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU 200 | 1.54178 | ||
2 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.08090 | NSLS | X29A |
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 | |||||||
1,2 | 1.65 | 50 | 92 | 0.039 | 0.048 | 19.3 | 2.8 | 59358 | 24741 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
1,2 | 1.65 | 1.81 | 73.3 | 0.256 | 0.17 | 2.23 | 1.9 | 1783 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 2ACG | 1.65 | 42 | 24740 | 1262 | 84.86 | 0.177 | 0.177 | 0.175 | 0.206 | RANDOM | 15.225 |
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] | |
1.78 | -0.85 | -1.37 | -0.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.257 |
r_dihedral_angle_3_deg | 16.026 |
r_dihedral_angle_4_deg | 14.438 |
r_dihedral_angle_1_deg | 5.045 |
r_scangle_it | 2.127 |
r_scbond_it | 1.515 |
r_angle_refined_deg | 1.255 |
r_mcangle_it | 0.856 |
r_angle_other_deg | 0.816 |
r_mcbond_it | 0.656 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1866 |
Nucleic Acid Atoms | |
Solvent Atoms | 265 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |