PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0014821-001
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.8 | 298 | 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.11 | 41.59 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.481 | α = 90 |
| b = 42.481 | β = 90 |
| c = 216.453 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 2 2 |
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 EIGER2 XE 9M | 2023-09-27 | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92124 | Diamond | I04-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.67 | 216.43 | 100 | 0.201 | 0.205 | 0.04 | 0.999 | 7.2 | 25.5 | 24396 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.67 | 1.7 | 99.1 | 16.48 | 3.181 | 0.487 | 26.2 | ||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.67 | 54.11 | 20309 | 1080 | 87.97 | 0.23672 | 0.23437 | 0.2469 | 0.28119 | 0.2833 | RANDOM | 55.224 | |||||
| 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] | |
| 1.8 | 1.8 | -3.6 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.34 |
| r_long_range_B_other | 23.074 |
| r_long_range_B_refined | 23.015 |
| r_dihedral_angle_4_deg | 17.55 |
| r_dihedral_angle_3_deg | 15.355 |
| r_dihedral_angle_1_deg | 7.919 |
| r_scangle_other | 4.309 |
| r_mcangle_it | 3.558 |
| r_mcangle_other | 3.558 |
| r_scbond_other | 2.631 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1476 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 97 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| BUSTER | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| XDS | data reduction |
| XDS | data reduction |
| XDS | data reduction |
| XDS | data reduction |
| XDS | data reduction |
