5MCQ
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH ACTIVE SITE AND EXOSITE BINDING PEPTIDE INHIBITOR
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 295 | 0.1M magnesium acetate, 0.1M sodium acetate, 8% (w/v) PEG8000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.65 | 66.27 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 101.93 | α = 90 |
| b = 101.93 | β = 90 |
| c = 116.35 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 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 | PIXEL | DECTRIS PILATUS 6M | 2016-02-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0000 | SLS | X10SA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.82 | 48.58 | 99.9 | 0.0813 | 16.7 | 10.24 | 63008 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.82 | 1.91 | 99.9 | 1.3 | 10.13 | ||||||||||||||
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 | THROUGHOUT | unpublished structure | 1.82 | 48.58 | 59801 | 3169 | 99.94 | 0.18007 | 0.17774 | 0.22424 | RANDOM | 33.565 | ||||||
| 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] | |
| 0.51 | 0.25 | 0.51 | -1.65 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.19 |
| r_dihedral_angle_4_deg | 17.696 |
| r_dihedral_angle_3_deg | 14.25 |
| r_long_range_B_refined | 9.087 |
| r_dihedral_angle_1_deg | 6.99 |
| r_mcangle_it | 4.347 |
| r_scbond_it | 4.197 |
| r_mcbond_it | 2.922 |
| r_angle_refined_deg | 1.932 |
| r_chiral_restr | 0.134 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3248 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 586 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
