2VKF
COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CCC | PDB ENTRY 2CCC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA HEPES PH 7.5 AND 30% PEG400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.41 | 63.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.704 | α = 90 |
b = 141.704 | β = 90 |
c = 141.704 | γ = 90 |
Symmetry | |
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Space Group | F 41 3 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 | MARRESEARCH | 2006-08-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | SLS | X10SA |
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 | 1.69 | 20 | 95.4 | 0.09 | 19.8 | 12.7 | 171130 | 3 |
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 | 1.69 | 1.8 | 79 | 0.52 | 4.1 | 8.4 |
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 2CCC | 1.7 | 19.03 | 12770 | 703 | 96.6 | 0.186 | 0.184 | 0.213 | RANDOM | 18.22 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.182 |
r_dihedral_angle_3_deg | 11.584 |
r_dihedral_angle_4_deg | 10.926 |
r_dihedral_angle_1_deg | 6.03 |
r_scangle_it | 3.717 |
r_scbond_it | 1.985 |
r_mcangle_it | 1.588 |
r_angle_refined_deg | 1.458 |
r_mcbond_it | 0.843 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 473 |
Nucleic Acid Atoms | |
Solvent Atoms | 86 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |