3NR6
Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | PROTEIN CONCENTRATION: 10 MG/ML PRECIPITANT: 0.06 M KH2PO4, 1.34 M NA2HPO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.9 | 35.11 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.915 | α = 90 |
b = 63.915 | β = 90 |
c = 106.509 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 4 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 | CCD | MARMOSAIC 300 mm CCD | MIRRORS | 2010-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.97 | 50 | 98.5 | 0.044 | 0.044 | 32.1 | 4.3 | 16141 | 16141 | -1.74 | -3 | 37.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.97 | 2 | 82.1 | 0.257 | 0.257 | 3.23 | 2.9 | 667 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | ASSEMBLY OF RETROVIRAL PROTEASES | 1.97 | 20 | 15336 | 815 | 98.46 | 0.19737 | 0.19737 | 0.19568 | 0.23322 | RANDOM | 47.871 |
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] | |
0.48 | 0.48 | -0.97 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.578 |
r_dihedral_angle_3_deg | 17.844 |
r_dihedral_angle_4_deg | 15.2 |
r_dihedral_angle_1_deg | 7.603 |
r_scangle_it | 5.066 |
r_mcangle_it | 4.062 |
r_scbond_it | 3.676 |
r_mcbond_it | 2.739 |
r_angle_refined_deg | 1.837 |
r_chiral_restr | 0.145 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1791 |
Nucleic Acid Atoms | |
Solvent Atoms | 66 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
Rosetta | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
Rosetta | phasing |