1S31
Crystal Structure Analysis of the human Tub protein (isoform a) spanning residues 289 through 561
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1C8Z | PDB ENTRY 1C8Z |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 277.2 | 16% PEG 400, 5mM Magnesium Chloride, 100mM Sodium Acetate, 15mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K, pH 5.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.56 | 73.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 149.981 | α = 90 |
b = 149.981 | β = 90 |
c = 149.981 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | 110 | CCD | MARRESEARCH | 2003-08-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 32-ID | 0.9814 | APS | 32-ID |
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 | 2.7 | 20 | 100 | 0.096 | 30.9 | 24 | 15560 | 15503 | -3 |
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 | 2.7 | 2.8 | 99.7 | 100 | 0.344 | 10.1 | 1511 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1C8Z | 2.704 | 18.474 | 14674 | 14674 | 767 | 100 | 0.1836 | 0.1814 | 0.2264 | Random | 33.802 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
Torsion angles, period 2. refined | 35.395 |
Torsion angles, period 4. refined | 21.636 |
Torsion angles, period 3. refined | 20.368 |
Torsion angles, period 1. refined | 7.722 |
S. chain angle B values: refined atoms | 3.361 |
S. chain bond B values: refined atoms | 1.952 |
M. chain angle B values: refined atoms | 1.903 |
Bond angles : refined atoms | 1.612 |
S. chain angle B values: others | 1.468 |
M. chain bond B values: refined atoms | 1.08 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2138 |
Nucleic Acid Atoms | |
Solvent Atoms | 90 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |