6F73
Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2IPI | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 |
experimental model | PDB | 2BVF | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 |
experimental model | PDB | 2Y08 | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 |
experimental model | PDB | 3W8W | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 |
experimental model | PDB | 3RJ8 | 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 |
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 | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.417 | α = 90 |
b = 115.959 | β = 90 |
c = 198.676 | γ = 90 |
Symmetry | |
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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 |