2CE9
A WRPW peptide bound to the Groucho-TLE WD40 domain.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GXR | PDB ENTRY 1GXR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.5 | 287 | 6MG/ML PROTEIN WAS MIXED 1:1 WITH 12% PEG8000, 100MM NACACODYLATE PH6.5, 100MM NAACETATE AT 14C IN MICROBATCH. PEPTIDES WERE ADDED TO THE PROTEIN CRYSTALS IN 125 MM NACL, 25 MM TRIS PH8.0, 0.5 MM EDTA TO A FINAL CONCENTRATION OF 0.76 MM, AND INCUBATED FOR 16 H BEFORE HARVESTING AND WASHING IN 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, AND CRYO-PROTECTED IN 30% ETHYLENE GLYCOL 50MM NA CACODYLATE PH6.5, 12 % PEG 8K, pH 6.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.81 | α = 90 |
b = 56.478 | β = 112.68 |
c = 126.642 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | OSMIC MIRRORS | 2005-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 |
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 | 2.12 | 45 | 97.5 | 0.06 | 13.4 | 3.4 | 78005 |
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 | 2.12 | 2.24 | 83 | 0.25 | 4.6 | 2.9 |
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 1GXR | 2.12 | 117.04 | 74067 | 3924 | 97.7 | 0.181 | 0.178 | 0.244 | RANDOM | 25.93 |
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] | |
-0.98 | -0.65 | 0.15 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.092 |
r_dihedral_angle_4_deg | 20.019 |
r_dihedral_angle_3_deg | 15.151 |
r_dihedral_angle_1_deg | 8.636 |
r_scangle_it | 3.857 |
r_scbond_it | 2.677 |
r_angle_refined_deg | 2.012 |
r_mcangle_it | 1.845 |
r_mcbond_it | 1.137 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10424 |
Nucleic Acid Atoms | |
Solvent Atoms | 861 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |