2HB4
Structure of HIV Protease NL4-3 in an Unliganded State
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 281.16 | 100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.92 | 57.92 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 48.985 | α = 90 |
| b = 48.985 | β = 90 |
| c = 105.62 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 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 | RIGAKU SATURN 92 | Rigaku VariMax HF Confocal Mirror | 2006-05-02 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | |||
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 | 2.15 | 44.44 | 99.7 | 0.095 | 8.9 | 7.34 | 13572 | 13526 | 2 | 3 | |||||||||
| 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 | 2.15 | 2.23 | 99.5 | 0.601 | 2.2 | 7.24 | 1334 | ||||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.15 | 44.46 | 7074 | 393 | 99.57 | 0.23834 | 0.23409 | 0.32073 | RANDOM | 38.072 | |||||||
| 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] | |
| 0.8 | 0.8 | -1.6 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 44.988 |
| r_dihedral_angle_4_deg | 17.376 |
| r_dihedral_angle_3_deg | 17.117 |
| r_dihedral_angle_1_deg | 10.26 |
| r_scangle_it | 7.613 |
| r_scbond_it | 5.677 |
| r_mcangle_it | 3.539 |
| r_mcbond_it | 2.54 |
| r_angle_refined_deg | 2.034 |
| r_symmetry_vdw_refined | 0.327 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 760 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 41 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOLREP | phasing |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data reduction |
| d*TREK | data scaling |
