3SMR
Crystal structure of human WD repeat domain 5 with compound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2O9K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 297 | 24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 204.171 | α = 90 |
b = 93.467 | β = 107.24 |
c = 64.786 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | RIGAKU RAXIS HTC | VeriMax HR | 2011-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54 |
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 | 1.82 | 50 | 100 | 0.086 | 25 | 7.2 | 104206 | 104206 | 23.1 |
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) | |||||||||||
1 | 1.82 | 1.85 | 100 | 0.807 | 2.12 | 6.4 | 5202 |
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 | 2O9K | 1.82 | 50 | 104206 | 103163 | 1043 | 99.77 | 0.17757 | 0.17759 | 0.17729 | 0.20612 | RANDOM | 25.61 |
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] | |
2.2 | 1.52 | -0.98 | -0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.519 |
r_dihedral_angle_4_deg | 23.264 |
r_dihedral_angle_3_deg | 13.264 |
r_dihedral_angle_1_deg | 6.844 |
r_scangle_it | 1.567 |
r_angle_refined_deg | 1.134 |
r_scbond_it | 0.988 |
r_mcangle_it | 0.645 |
r_mcbond_it | 0.35 |
r_chiral_restr | 0.076 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9233 |
Nucleic Acid Atoms | |
Solvent Atoms | 822 |
Heterogen Atoms | 228 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |