6L1X
Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 277 | 50 mM HEPES pH8 26% PEG 600 (v/v) 0.5 mM zinc sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.17 | 70.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.12 | α = 90 |
b = 116.68 | β = 90 |
c = 123.55 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | CCD | RAYONIX MX300HE | 2017-05-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
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 | 3.1 | 49.92 | 83.3 | 0.113 | 0.141 | 0.064 | 0.997 | 6.5 | 4.1 | 19034 | 61 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.1 | 3.31 | 84.5 | 0.556 | 0.7 | 0.42 | 0.284 | 2.2 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MIR | THROUGHOUT | 3.15 | 49.92 | 19034 | 1063 | 81.46 | 0.25313 | 0.25029 | 0.30253 | RANDOM | 100.951 |
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] | |
-5.94 | 0.18 | 5.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.285 |
r_dihedral_angle_3_deg | 19.755 |
r_dihedral_angle_4_deg | 14.511 |
r_long_range_B_refined | 13.719 |
r_mcangle_it | 8.12 |
r_dihedral_angle_1_deg | 6.296 |
r_scbond_it | 5.069 |
r_mcbond_it | 4.881 |
r_angle_refined_deg | 0.999 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5562 |
Nucleic Acid Atoms | |
Solvent Atoms | 1 |
Heterogen Atoms | 91 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |