3K6L
The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 294 | 20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.84 | 56.74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 73.96 | α = 90 |
| b = 73.96 | β = 90 |
| c = 241.5 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 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 | ADSC QUANTUM 315 | Si (111) double crystal monochromator. Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing | 2009-08-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.9795 | Diamond | I02 |
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 | 2.15 | 241.5 | 90.8 | 0.069 | 0.064 | 8.4 | 7.5 | 37679 | 1.6 | 36.6 | |||||||||
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 | PDB entry 1G27 | 2.15 | 241.5 | 32520 | 1690 | 90.79 | 0.26113 | 0.2582 | 0.31919 | RANDOM | 47.589 | ||||||
| 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] | |
| -0.74 | -0.74 | 1.48 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.358 |
| r_dihedral_angle_4_deg | 17.258 |
| r_dihedral_angle_3_deg | 16.148 |
| r_dihedral_angle_1_deg | 5.396 |
| r_scangle_it | 2.266 |
| r_scbond_it | 1.294 |
| r_angle_refined_deg | 1.162 |
| r_mcangle_it | 1.097 |
| r_mcbond_it | 0.594 |
| r_chiral_restr | 0.073 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3854 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 233 |
| Heterogen Atoms | 51 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DNA | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
