2VDY
Crystal structure of the reactive loop cleaved Corticosteroid Binding Globulin complexed with Cortisol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QMN | PDB ENTRY 1QMN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.4 | 10-20% PEG3350, 0.2M NACL, pH 7.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 34 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 38.673 | ¦Á = 83.09 |
b = 39.757 | ¦Â = 85.7 |
c = 111.586 | ¦Ã = 69.42 |
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 | IMAGE PLATE | MARRESEARCH | 2007-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 2.3 | 19.4 | 93.5 | 0.08 | 11 | 2.2 | 22575 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.3 | 2.42 | 91.1 | 0.46 | 2.5 | 2.2 |
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 1QMN | 2.3 | 19.43 | 24274 | 1295 | 93.5 | 0.213 | 0.21 | 0.271 | RANDOM | 28.75 |
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] | |
1.04 | 0.29 | 1.45 | 1.36 | 0.74 | -2.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.446 |
r_dihedral_angle_3_deg | 14.435 |
r_dihedral_angle_4_deg | 12.732 |
r_dihedral_angle_1_deg | 5.063 |
r_angle_refined_deg | 0.969 |
r_scangle_it | 0.498 |
r_scbond_it | 0.318 |
r_mcangle_it | 0.308 |
r_nbtor_refined | 0.294 |
r_mcbond_it | 0.18 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5670 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |