1PB1
A four location model to explain the stereospecificity of proteins.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 295 | IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.38 | 71.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 103.654 | ¦Á = 90 |
b = 103.654 | ¦Â = 90 |
c = 149.391 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | CCD | ADSC QUANTUM 4 | 1999-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.0 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.7 | 25 | 92.7 | 91206 | 83266 | 17.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 1.76 | 84.6 | 0.212 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.7 | 24.79 | 74903 | 83226 | 8363 | 92.7 | 0.185 | 0.185 | 0.185 | 0.211 | RANDOM | 21.4 |
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] | |
2.09 | 2.09 | -4.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25 |
c_scangle_it | 3.84 |
c_scbond_it | 2.48 |
c_mcangle_it | 2 |
c_angle_deg | 1.6 |
c_mcbond_it | 1.31 |
c_improper_angle_d | 1.02 |
c_bond_d | 0.015 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3213 |
Nucleic Acid Atoms | |
Solvent Atoms | 337 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |