6UVF
Crystal structure of BCL-XL bound to compound 12: (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl)propanoic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 1.4 M ammonium sulfate, 0.1 M MES pH 6.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.31 | 46.77 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 92.386 | α = 90 |
b = 104.65 | β = 110.99 |
c = 110.076 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
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 | ADSC QUANTUM 315r | 2016-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.24 | 47.52 | 99.4 | 0.069 | 0.074 | 0.999 | 18.2 | 7.517 | 93096 | 54.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.24 | 2.38 | 97.3 | 0.957 | 1.029 | 0.802 | 1.99 | 7.43 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2YXJ | 2.24 | 47.52 | 93094 | 4655 | 99.5 | 0.201 | 0.2 | 0.227 | RANDOM | 74.21 |
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] | |
5.7994 | -5.8733 | -7.4354 | 1.636 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 17.4 |
t_omega_torsion | 2.63 |
t_angle_deg | 0.95 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 13445 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 630 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
BUSTER | refinement |
PDB_EXTRACT | data extraction |