2YLS
SNAPSHOTS OF ENZYMATIC BAEYER-VILLIGER CATALYSIS: OXYGEN ACTIVATION AND INTERMEDIATE STABILIZATION: REDUCED ENZYME BOUND TO NADP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6.5 | 277 | BY VAPOR-DIFFUSION AT 4 DEGREES C USING 1-3 MICROL OF PROTEIN SOLUTIONS (18 MG/ML IN 0.5 MICROM FAD AND 4 MM NADP, 50 MM TRIS/HCL PH 7.5) MIXED WITH EQUAL VOLUMES OF RESERVOIR CONTAINING 40% W/V PEG4000, 100 MM MES/HCL PH 6.5, AND 100 MM NACL. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.93 | 40 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 107.92 | α = 90 |
| b = 107.92 | β = 90 |
| c = 106.83 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 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 | CCD | ADSC QUANTUM 210 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 | |
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 | 2.26 | 30 | 99.6 | 0.09 | 8.7 | 3 | 34153 | ||||||||||||
| 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 | 2.26 | 2.4 | 98.8 | 0.3 | 3.4 | 2.9 | |||||||||||||
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 2YLR | 2.26 | 42.81 | 32332 | 1676 | 99.18 | 0.18932 | 0.18692 | 0.23549 | RANDOM | 23.467 | ||||||
| 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] | |
| 1.39 | 0.69 | 1.39 | -2.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.783 |
| r_dihedral_angle_4_deg | 19.619 |
| r_dihedral_angle_3_deg | 16.261 |
| r_dihedral_angle_1_deg | 6.577 |
| r_scangle_it | 4.798 |
| r_scbond_it | 3.111 |
| r_angle_refined_deg | 1.881 |
| r_mcangle_it | 1.735 |
| r_mcbond_it | 0.953 |
| r_chiral_restr | 0.125 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4230 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 238 |
| Heterogen Atoms | 101 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
