2XWY
Structure of MK-3281, a Potent Non-Nucleoside Finger-Loop Inhibitor, in complex with the Hepatitis C Virus NS5B Polymerase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | 277 | SOAKING WITH COMPOUND MK3281 WAS PERFORMED AT 4 DEG C BY TRANSFERRING THE APO-NS5B CRYSTALS FOR 10 MIN IN A SOLUTION CONTAINING 100 MM 2-MORPHOLINOETHANESULFONIC ACID (MES), PH 6.0, 14% POLYETHYLENE GLYCOL (PEG) 8,000, 14% 2- PROPANOL, 2.5 MM TCEP, 10 MM MNCL2 AND 2.5 MM OF COMPOUND MK3281. THE CRYSTALS WERE THEN TRANSFERRED FOR 1 MIN TO A CRYO-PROTECTANT SOLUTION CONTAINING 100 MM MES PH 6.0, 14% POLYETHYLENE GLYCOL PEG 8,000, 14% 2-PROPANOL, 18% 2-METHYL-2,5 PENTANEDIOL (MPD), 2.5 MM TCEP, 5 MM MNCL2 AND 1.25 MM COMPOUND MK3281 AND THEN PLUNGED DIRECTLY INTO LIQUID NITROGEN. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 53 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 66.983 | α = 90 |
b = 94.272 | β = 90 |
c = 95.145 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 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 | CCD | ADSC QUANTUM 210 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.53 | 20 | 99.7 | 0.09 | 5.9 | 3.9 | 20692 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.53 | 2.67 | 99.7 | 0.53 | 1.5 | 3.8 |
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 | PDB ENTRY 1CSJ | 2.53 | 95.35 | 19605 | 1056 | 99.63 | 0.23727 | 0.23332 | 0.31016 | RANDOM | 54.851 |
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] | |
1.15 | -5.32 | 4.17 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.962 |
r_dihedral_angle_3_deg | 18.535 |
r_dihedral_angle_4_deg | 17.26 |
r_dihedral_angle_1_deg | 5.734 |
r_scangle_it | 2.504 |
r_scbond_it | 1.543 |
r_angle_refined_deg | 1.349 |
r_mcangle_it | 0.916 |
r_mcbond_it | 0.468 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3911 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 37 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |