2NPD
An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XQF | PDB ENTRY 1XQF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 298 | 30% PEG 550, 0.1M SODIUM ACETATE, 0.2M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 4.60 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.305 | α = 90 |
b = 109.305 | β = 90 |
c = 84.404 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | MARMOSAIC 225 mm CCD | 2005-11-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.98017 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.1 | 50 | 99.2 | 0.069 | 14.86 | 33268 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.2 | 99.7 | 0.564 | 3.55 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1XQF | 2.1 | 15 | 33439 | 31547 | 1683 | 99.37 | 0.17324 | 0.17324 | 0.17197 | 0.19787 | RANDOM | 46.932 |
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] | |
2.55 | 1.27 | 2.55 | -3.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.602 |
r_dihedral_angle_4_deg | 21.62 |
r_dihedral_angle_3_deg | 14.76 |
r_scangle_it | 4.923 |
r_scbond_it | 3.554 |
r_mcangle_it | 2.342 |
r_dihedral_angle_1_deg | 1.819 |
r_angle_refined_deg | 1.526 |
r_mcbond_it | 1.509 |
r_nbtor_refined | 0.322 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2685 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
MAR345 | data collection |
XDS | data reduction |
XSCALE | data scaling |