6F73
Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 294 | 20% PEG6000, , 0.2 M NaCl, 0.1 M NaAcetate pH 5.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.9 | 57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 62.417 | α = 90 |
| b = 115.959 | β = 90 |
| c = 198.676 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 2 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 | 110 | IMAGE PLATE | MARRESEARCH | 2015-01-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.22 | 58 | 99.5 | 0.147 | 0.081 | 0.995 | 12.9 | 8 | 71982 | 13.9 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.22 | 2.27 | 92.8 | 0.514 | 0.225 | 0.706 | 3.7 | 6.7 | |||||||||||
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 | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 | 2.22 | 58 | 68291 | 3610 | 99.48 | 0.19489 | 0.1928 | 0.23467 | RANDOM | 36.81 | ||||||
| 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] | |
| 0.03 | 0.46 | -0.49 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.009 |
| r_dihedral_angle_4_deg | 16.002 |
| r_dihedral_angle_3_deg | 12.926 |
| r_long_range_B_other | 9.446 |
| r_long_range_B_refined | 9.431 |
| r_scangle_other | 7.105 |
| r_scbond_it | 5.97 |
| r_dihedral_angle_1_deg | 5.969 |
| r_scbond_other | 5.969 |
| r_angle_other_deg | 3.844 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8364 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 847 |
| Heterogen Atoms | 260 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
