9DUE
Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-07-081a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4YPD |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 292 | Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM SRM-7-081a, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.93 | 36.22 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 47.01 | α = 90 |
b = 62.684 | β = 90 |
c = 88.462 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2019-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | 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 | 1.65 | 30 | 100 | 0.057 | 0.057 | 0.062 | 0.023 | 0.998 | 28.3 | 7.2 | 32407 | -3 | 22.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.65 | 1.68 | 100 | 0.881 | 0.881 | 0.961 | 0.378 | 0.683 | 2.1 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.65 | 29.54 | 30598 | 1577 | 99.97 | 0.15521 | 0.15375 | 0.18352 | RANDOM | 26.461 |
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] | |
-0.1 | 0.66 | -0.56 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_long_range_B_refined | 7.834 |
r_dihedral_angle_3_deg | 7.616 |
r_long_range_B_other | 7.612 |
r_scangle_other | 6.092 |
r_scbond_it | 4.028 |
r_scbond_other | 3.851 |
r_dihedral_angle_1_deg | 3.496 |
r_mcangle_it | 2.954 |
r_mcangle_other | 2.954 |
r_mcbond_it | 2.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2238 |
Nucleic Acid Atoms | |
Solvent Atoms | 202 |
Heterogen Atoms | 49 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |