1A3Q
HUMAN NF-KAPPA-B P52 BOUND TO DNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | THE PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE RESERVOIR SOLUTION CONTAINED 5% PEG 4000, 5 MM MGSO4, 50 MM MES PH 6.0 AND 3 MM DTT. DROPS CONTAINED A 1:1 MIXTURE OF COMPLEX SOLUTION AND RESERVOIR SOLUTION., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.2 | α = 90 |
b = 121 | β = 90 |
c = 134.9 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 120 | IMAGE PLATE | MARRESEARCH | MIRRORS | 1996-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 2.1 | 20 | 91.8 | 6.1 | 10.5 | 3.1 | 39642 | 39.9 |
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) | |||||||||||
2.1 | 2.2 | 78.1 | 31.2 | 2.63 | 2.1 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | MODIFIED HUMAN NF-KAPPAB P50-DNA COMPLEX, PDB ENTRY | 2.1 | 10 | 39039 | 3805 | 91.8 | 0.219 | 0.32 | RANDOM | 47.8 |
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] | |
-5.7 | 8.4 | -2.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_scangle_it | 6.85 |
x_mcangle_it | 5.55 |
x_scbond_it | 5.28 |
x_mcbond_it | 3.87 |
x_angle_deg | 2.1 |
x_improper_angle_d | 1.64 |
x_bond_d | 0.013 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4518 |
Nucleic Acid Atoms | 445 |
Solvent Atoms | 785 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |