4DOX
Crystal Structure of Papaya mosaic virus capsid protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.6 | 277 | 100 mM Hepes, 9% PEG 6000, pH 7.6, VAPOR DIFFUSION, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.1 | 41.39 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 72.943 | α = 90 |
b = 72.943 | β = 90 |
c = 133.325 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 |
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 315 | 2011-02-10 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2011-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1000 | NSLS | X25 |
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.0082 | NSLS | X25 |
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 | |||||||
1,2 | 2.7 | 45 | 99 | 0.129 | 0.109 | 16.7 | 8.5 | 11087 | 11047 | 2 | 2 |
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) | ||||||||||
1,2 | 2.7 | 2.75 | 99 | 0.446 | 0.414 | 4.2 | 8.3 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 2.7 | 30 | 10502 | 529 | 99.87 | 0.17117 | 0.16838 | 0.22848 | RANDOM | 40.274 |
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] | |
0.81 | 0.4 | 0.81 | -1.21 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.644 |
r_dihedral_angle_4_deg | 21.66 |
r_dihedral_angle_3_deg | 18.579 |
r_dihedral_angle_1_deg | 6.557 |
r_scangle_it | 4.112 |
r_scbond_it | 2.411 |
r_mcangle_it | 1.791 |
r_angle_refined_deg | 1.71 |
r_mcbond_it | 0.944 |
r_chiral_restr | 0.111 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2468 |
Nucleic Acid Atoms | |
Solvent Atoms | 153 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
CBASS | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |