7YCT
HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 0.1 M BIS-TRIS (pH 5.5), 2.0 M ammonium sulfate incubated in 25% (v/v) glycerol with a drop of (R)-2-Chlorobenzaldehyde, and soaked with 2 M potassium cyanide | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.51 | 64.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 123.79 | ¦Á = 90 |
| b = 123.79 | ¦Â = 90 |
| c = 129.5 | ¦Ã = 120 |
| Symmetry | |
|---|---|
| Space Group | P 63 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 293.15 | IMAGE PLATE | RIGAKU | 2017-08-16 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
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 | 2.01 | 61.9 | 99.2 | 0.052 | 10.4 | 3 | 74391 | ||||||||||||
| 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 | 2.01 | 2.05 | 0.294 | ||||||||||||||||
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6KFE | 2.01 | 53.66 | 74380 | 3627 | 99.21 | 0.172 | 0.171 | 0.1996 | 29.239 | |||||||
| 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] | |
| 0.007 | 0.004 | 0.007 | -0.024 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_6_deg | 16.829 |
| r_dihedral_angle_3_deg | 15.095 |
| r_dihedral_angle_2_deg | 10.387 |
| r_dihedral_angle_1_deg | 7.708 |
| r_lrange_it | 7.662 |
| r_lrange_other | 7.581 |
| r_scangle_it | 6.149 |
| r_scangle_other | 5.973 |
| r_scbond_it | 4.497 |
| r_scbond_other | 4.326 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5055 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 474 |
| Heterogen Atoms | 121 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| Coot | model building |
