1J75
Crystal Structure of the DNA-Binding Domain Zalpha of DLM-1 Bound to Z-DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QBJ | PDB ENTRY 1QBJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 297 | 15% PEG 4000, 0.1M ammonium hydrogen phosphate, 15% ethylene glycol, 0.1M MES pH 6.0, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.611 | α = 90 |
b = 63.611 | β = 90 |
c = 72.238 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | MARRESEARCH | 2000-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.9102 | EMBL/DESY, HAMBURG | X11 |
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 | 1.85 | 32 | 99.8 | 0.066 | 6.7 | 23.4 | 7802 | 7802 | 37.6 |
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) | |||||||||||
1.85 | 1.88 | 99.5 | 0.613 | 2.9 | 7.9 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1QBJ | 1.85 | 32 | 7778 | 7778 | 826 | 99.53 | 0.225 | 0.225 | 0.218 | 0.24 | RANDOM R VALUE (WORKING + TEST SET) : 0.22152 | 21.3 |
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] | |
0.08 | 0.04 | 0.08 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_mcangle_it | 2.6 |
c_angle_deg_na | 1.8 |
c_mcbond_it | 1.61 |
c_angle_deg | 1.59 |
c_bond_d | 0.019 |
c_bond_d_na | 0.017 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 444 |
Nucleic Acid Atoms | 140 |
Solvent Atoms | 102 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
EPMR | phasing |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |