1FMJ
CRYSTAL STRUCTURE OF MERCURY DERIVATIVE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINOL AND PAP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BO6 | polyalanine model derived from estrogen sulfotransferase |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.6 | 284 | PEG 3350, calcium chloride, Hepes, glycerol, EMTS, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 49.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.429 | α = 90 |
b = 66.183 | β = 108.89 |
c = 83.336 | 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 | 103 | CCD | 1999-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-D | APS | 14-BM-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 | 2 | 30 | 88.1 | 0.084 | 19.5 | 2.95 | 102345 | 48540 | -3 | 18.8 |
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) | |||||||||||
2 | 2.05 | 84.6 | 0.227 | 6.58 | 2.34 | 3428 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1FMJ | 2 | 30 | 69313 | 46863 | 3576 | 88.1 | 0.231 | 0.264 | random | 25.9 |
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] | |
1.32 | -2.26 | -0.38 | -0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 1.85 |
c_mcangle_it | 1.35 |
c_scbond_it | 1.31 |
c_angle_deg | 1.3 |
c_mcbond_it | 0.85 |
c_improper_angle_d | 0.81 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5644 |
Nucleic Acid Atoms | |
Solvent Atoms | 273 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |