3OJN
Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase at 1.65 Ang resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IG9 | PDB entry 2IG9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 13% PEG6000, 0.125 M calcium chloride, 0.1 M Tris-HCl, Cryoprotectant 25% PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.08 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 110.542 | ¦Á = 90 |
b = 151.497 | ¦Â = 90 |
c = 96.359 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 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 315r | 2010-08-04 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2010-08-04 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2010-08-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.8923 | Diamond | I03 |
3 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.8958 | Diamond | I03 |
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 | |||||||
1,2,3 | 1.65 | 29.78 | 97.6 | 0.061 | 0.094 | 7.3 | 3.2 | 193414 | 188772 | 3 | 16.4 |
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) | ||||||||||
1.65 | 1.74 | 98.5 | 0.357 | 0.552 | 2 | 3.2 | 27593 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2IG9 | 1.65 | 29.77 | 179300 | 9422 | 97.25 | 0.14932 | 0.14789 | 0.17662 | RANDOM | 20.512 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.03 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.617 |
r_dihedral_angle_4_deg | 17.656 |
r_dihedral_angle_3_deg | 11.996 |
r_dihedral_angle_1_deg | 6.93 |
r_scangle_it | 3.315 |
r_scbond_it | 2.091 |
r_angle_refined_deg | 1.403 |
r_mcangle_it | 1.236 |
r_angle_other_deg | 0.902 |
r_mcbond_it | 0.717 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11532 |
Nucleic Acid Atoms | |
Solvent Atoms | 1379 |
Heterogen Atoms | 143 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |