5OHB
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidin-2-one (Valerolactam)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4V2Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.8 | 30 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.517 | α = 90 |
b = 59.63 | β = 90 |
c = 88.557 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2015-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.7 | 37.2 | 99.2 | 0.047 | 1 | 13.3 | 3.23 | 33597 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.8 | 97.7 | 0.49 | 0.84 | 2.11 | 3.2 |
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 | 4V2Y | 1.7 | 37.2 | 31914 | 1679 | 99.6 | 0.17128 | 0.16918 | 0.21175 | RANDOM | 37.226 |
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] | |
-0.28 | 1.8 | -1.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.403 |
r_dihedral_angle_4_deg | 13.401 |
r_dihedral_angle_3_deg | 12.378 |
r_long_range_B_refined | 6.975 |
r_long_range_B_other | 6.914 |
r_dihedral_angle_1_deg | 6.292 |
r_scangle_other | 3.8 |
r_scbond_it | 2.498 |
r_scbond_other | 2.498 |
r_mcangle_it | 2.452 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2434 |
Nucleic Acid Atoms | |
Solvent Atoms | 152 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |