6F9Q
Binary complex of a 7S-cis-cis-nepetalactol cyclase from Nepeta mussinii with NAD+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | NULL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.921 | α = 90 |
b = 107.75 | β = 104.26 |
c = 69.361 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2017-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.4 | 47.16 | 98.6 | 0.09 | 0.097 | 0.037 | 0.999 | 11.2 | 6.9 | 175909 | 14.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.4 | 1.42 | 97 | 1.564 | 1.69 | 0.637 | 0.561 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2BGK | 1.4 | 47.16 | 167049 | 8822 | 98.51 | 0.1513 | 0.1505 | 0.1682 | RANDOM | 18.4 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.71 | 0.02 | -0.33 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.919 |
r_dihedral_angle_3_deg | 11.61 |
r_dihedral_angle_1_deg | 5.601 |
r_angle_refined_deg | 1.562 |
r_angle_other_deg | 0.945 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.002 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7529 |
Nucleic Acid Atoms | |
Solvent Atoms | 1109 |
Heterogen Atoms | 184 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |