6XTE
Human karyopherin RanBP5 (isoform-1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3W3U |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 100 mM tri-sodium citrate pH 4.5, 12 % PEG 6000, 100 mM ammonium acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.091 | α = 90 |
b = 96.313 | β = 90 |
c = 156.979 | 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 PILATUS3 6M | 2016-06-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.00000 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 2.27 | 48 | 70.3 | 0.089 | 0.046 | 0.996 | 9.3 | 4.4 | 181499 | 41396 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.27 | 2.54 | 14.5 | 0.892 | 0.452 | 0.68 | 1.7 | 4.3 |
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 | 3W3U | 2.27 | 78.49 | 41396 | 2155 | 67.1 | 0.2019 | 0.1988 | 0.2595 | RANDOM | 71.91 |
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] | |
8.6076 | -8.0098 | -0.5978 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 19.34 |
t_omega_torsion | 2.76 |
t_angle_deg | 0.97 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8446 |
Nucleic Acid Atoms | |
Solvent Atoms | 84 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |