Crystal structure of halogenase CtcP from Kitasatospora aureofaciens in complex with FAD
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6BZQ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 294 | 26% PEG 4000, 100 mM Hepes pH 7.5, 200 mM lithium sulfate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.3 | 46.49 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 62.764 | α = 90 |
| b = 103.576 | β = 95.4 |
| c = 179.216 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2019-10-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 50 | 96.9 | 0.137 | 0.982 | 15 | 3.5 | 121382 | 2 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.15 | 2.19 | 0.796 | 0.685 | |||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6BZQ | 2.15 | 35 | 114137 | 6167 | 96.91 | 0.1902 | 0.1879 | 0.19 | 0.2327 | 0.24 | RANDOM | 29.503 | ||||
| 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] | |
| 3.14 | -0.76 | -1.3 | -1.66 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.339 |
| r_dihedral_angle_4_deg | 15.213 |
| r_dihedral_angle_3_deg | 13.908 |
| r_dihedral_angle_1_deg | 6.543 |
| r_angle_refined_deg | 1.234 |
| r_angle_other_deg | 1.159 |
| r_chiral_restr | 0.05 |
| r_bond_refined_d | 0.004 |
| r_gen_planes_refined | 0.004 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 16973 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 942 |
| Heterogen Atoms | 263 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
