7B51
Crystal structure of human CRM1 covalently modified by 2-mercaptoethanol at Cys528
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TVO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 277.15 | 0.02M sodium L-glutamate, 0.02M DL-alanine, 0.02M glycine, 0.02M DL-lysine HCl, 0.02 M DL-serine, 10%w/v PEG 8000, 20% v/v ethylene glycol, 0.1M bicine /Trizma base pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.7 | 66.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 121.111 | α = 90 |
b = 150.591 | β = 90 |
c = 231.969 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | PIXEL | DECTRIS PILATUS 6M | 2019-05-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9762 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.58 | 126.31 | 97.5 | 0.077 | 0.083 | 0.999 | 16.6 | 7.964 | 65209 | 64.724 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.58 | 2.74 | 84.3 | 0.648 | 0.712 | 0.817 | 1.95 | 5.357 |
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 | FREE R-VALUE | 6TVO | 2.58 | 126.31 | 61972 | 3237 | 97.47 | 0.216 | 0.2142 | 0.25 | RANDOM | 62.109 |
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] | |
-1.46 | 3.67 | -2.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.025 |
r_dihedral_angle_3_deg | 17.764 |
r_dihedral_angle_4_deg | 17.666 |
r_dihedral_angle_1_deg | 5.856 |
r_angle_refined_deg | 1.605 |
r_chiral_restr | 0.133 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9613 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |