3FEK
Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic acid-binding protein II at 1.51 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G7B | PDB entry 2G7B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.1M Tris, 0.2M NaOAc, 24% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.38 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 34.601 | ¦Á = 73.64 |
b = 37.189 | ¦Â = 76.67 |
c = 57.056 | ¦Ã = 87.7 |
Symmetry | |
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Space Group | P 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 | 2007-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97850 | APS | 21-ID-G |
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 | 1.51 | 53.5 | 93.3 | 0.041 | 46.2 | 4.2 | 39062 | 1 | 29.6 |
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 | 1.51 | 1.56 | 70.5 | 0.232 | 4.5 | 3.4 | 2938 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2G7B | 1.51 | 33.66 | 37100 | 1961 | 94.25 | 0.17579 | 0.17579 | 0.17385 | 0.18 | 0.21028 | 0.21 | RANDOM | 29.467 |
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] | |
-0.65 | -0.57 | 0.36 | -2.68 | 0.57 | 2.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.549 |
r_dihedral_angle_4_deg | 16.387 |
r_dihedral_angle_3_deg | 13.856 |
r_sphericity_free | 5.885 |
r_dihedral_angle_1_deg | 5.74 |
r_sphericity_bonded | 5.069 |
r_scangle_it | 3.006 |
r_mcangle_it | 2.913 |
r_scbond_it | 2.334 |
r_rigid_bond_restr | 2.316 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2170 |
Nucleic Acid Atoms | |
Solvent Atoms | 318 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |