7NDX
Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 298 | 0.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.5 | 64.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.3 | α = 90 |
b = 128.264 | β = 90 |
c = 135.213 | γ = 90 |
Symmetry | |
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Space Group | I 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 | 193 | PIXEL | DECTRIS PILATUS 2M-F | 2020-02-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.0 | SLS | X06DA |
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 | 2.54 | 46.53 | 99.9 | 0.14 | 0.99 | 16.5 | 13 | 12295 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.54 | 2.65 | 0.66 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3AGY | 2.541 | 46.53 | 12295 | 607 | 99.911 | 0.235 | 0.2328 | 0.2681 | 69.028 |
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] | |
-3.914 | 2.607 | 1.307 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.139 |
r_dihedral_angle_4_deg | 21.374 |
r_dihedral_angle_3_deg | 18.674 |
r_dihedral_angle_1_deg | 8.467 |
r_lrange_it | 5.915 |
r_lrange_other | 5.914 |
r_scangle_it | 3.895 |
r_scangle_other | 3.895 |
r_mcangle_it | 3.57 |
r_mcangle_other | 3.568 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1430 |
Nucleic Acid Atoms | |
Solvent Atoms | 22 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |