3WNF
Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5MM CADMIUM CHLORIDE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.08 | 40.94 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 50.07 | α = 90 |
b = 50.07 | β = 90 |
c = 102.57 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 32 |
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 315r | MIRRORS | 2009-09-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.954 | Australian Synchrotron | MX2 |
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 | 1.45 | 50 | 94.4 | 0.038 | 0.043 | 22.7 | 5.5 | 51039 | 48158 | 263341 |
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 | 1.45 | 1.5 | 86.1 | 0.426 | 0.471 | 3.7 | 5.5 | 23206 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 3L3U | 1.45 | 43.36 | 51039 | 47703 | 2511 | 100 | 0.20056 | 0.1989 | 0.23226 | RANDOM | 17.128 |
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] | |
0.93 | 0.47 | 0.93 | -1.4 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.235 |
r_dihedral_angle_3_deg | 14.627 |
r_dihedral_angle_4_deg | 10.151 |
r_dihedral_angle_1_deg | 6.722 |
r_scangle_it | 6.093 |
r_scbond_it | 3.749 |
r_mcangle_it | 2.749 |
r_angle_refined_deg | 2.437 |
r_mcbond_it | 1.734 |
r_angle_other_deg | 1.116 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2161 |
Nucleic Acid Atoms | |
Solvent Atoms | 148 |
Heterogen Atoms | 36 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |