4QBJ
Crystal structure of N-myristoyl transferase from Aspergillus fumigatus complexed with a synthetic inhibitor
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1IIC | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 298 | 1.85-2.3M ammonium sulfate, 0.1M HEPES, 20mM MnCl2, 1mM TCEP, pH 7.1-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.61 | 52.93 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 54.792 | α = 90 |
| b = 77.074 | β = 90 |
| c = 113.237 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | IMAGE PLATE | RIGAKU RAXIS IIC | 2003-10-30 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | 1.542 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.1 | 100 | 28569 | ||||||||||||||||
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 | 1IIC | 2.1 | 25 | 27147 | 1421 | 99.59 | 0.17865 | 0.17669 | 0.21745 | RANDOM | 36.839 | ||||||
| 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] | |
| 0.56 | 0.02 | -0.59 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.487 |
| r_dihedral_angle_4_deg | 18.75 |
| r_dihedral_angle_3_deg | 15.028 |
| r_long_range_B_refined | 9.699 |
| r_dihedral_angle_1_deg | 6.188 |
| r_scbond_it | 5.706 |
| r_mcangle_it | 4.968 |
| r_mcbond_it | 3.63 |
| r_angle_refined_deg | 2.081 |
| r_chiral_restr | 0.141 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3140 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 146 |
| Heterogen Atoms | 112 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOLREP | phasing |
| REFMAC | refinement |
| d*TREK | data reduction |
| d*TREK | data scaling |
