4R3W
Crystal Structure Analysis of the 1,2,3-tricarboxylate benzoic acid bound to sp-ASADH-2'5'-ADP complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PWK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | 15-22% PEG, 0.1 M Na acetate, 0.1 M MES (pH 6.5), 10 mM TCEP, 3% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.82 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 59.964 | ¦Á = 90 |
b = 98.444 | ¦Â = 102.43 |
c = 64.263 | ¦Ã = 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 | 100 | CCD | MARMOSAIC 300 mm CCD | double crystal monochromator and K-B pair of biomorph mirrors | 2012-11-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.033 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.9 | 50 | 87 | 0.074 | 12.7 | 2.7 | 55400 | 49341 | 1 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.97 | 0.301 | 2.8 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | FOURIER SYNTHESIS | THROUGHOUT | 3PWK | 1.91 | 62.76 | 56700 | 46838 | 2490 | 86.63 | 0.188 | 0.18587 | 0.22892 | RANDOM | 37.345 |
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] | |
0.47 | 0.82 | 2.64 | -3.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.293 |
r_dihedral_angle_4_deg | 17.918 |
r_dihedral_angle_3_deg | 13.729 |
r_dihedral_angle_1_deg | 6.115 |
r_long_range_B_refined | 4.954 |
r_long_range_B_other | 4.919 |
r_scangle_other | 3.669 |
r_mcangle_it | 2.761 |
r_mcangle_other | 2.724 |
r_scbond_other | 2.325 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5366 |
Nucleic Acid Atoms | |
Solvent Atoms | 180 |
Heterogen Atoms | 104 |
Software
Software | |
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Software Name | Purpose |
Blue-ray | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |