1GU4
Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GTW | PDB ENTRY 1GTW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6 | 0.2 M POTASSIUM CHLORIDE, 0.01 M MAGNESIUM SULFATE, 10.0% V/V PEG 400, 0.05 M MES BUFFER PH 6.0, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML AND CONTAINS 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2. FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.69 | 66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.947 | α = 90 |
b = 112.326 | β = 90 |
c = 74.401 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 90 | IMAGE PLATE | RIGAKU RAXIS V | MIRRORS | 2001-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL45XU | SPring-8 | BL45XU |
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 | 1.75 | 30 | 99.4 | 0.094 | 21.7331 | 5.452 | 42716 | 31.9 |
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 | 1.75 | 1.78 | 98.3 | 0.455 | 2.079 | 3.96 |
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 1GTW | 1.8 | 29.95 | 39097 | 1916 | 99 | 0.232 | 0.232 | 0.266 | RANDOM | 39.9 |
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] | |
6.9 | -3.12 | -3.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 15 |
c_scangle_it | 7.83 |
c_scbond_it | 5.65 |
c_mcangle_it | 4.71 |
c_mcbond_it | 4.11 |
c_improper_angle_d | 0.96 |
c_angle_deg | 0.8 |
c_bond_d | 0.004 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1129 |
Nucleic Acid Atoms | 650 |
Solvent Atoms | 311 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |