4K5E
Structure of neuronal nitric oxide synthase heme domain in complex with (R)-1,2-bis((2-amino-4-methylpyridin-6-yl)-methoxy)-propan-3-amine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OM4 | PDB ENTRY 1OM4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | 277 | 20-22% PEG3350, 0.1 M MES, 0.14-0.20 M ammonium acetate, 10% ethylene glycol, 5 mM GSH, 30 uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.29 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.996 | ¦Á = 90 |
b = 110.666 | ¦Â = 90 |
c = 164.391 | ¦Ã = 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 | MARMOSAIC 325 mm CCD | Rh coated flat mirror, toroidal focusing mirror | 2011-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 1.000 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.892 | 50 | 99.2 | 0.054 | 0.054 | 29.9 | 4 | 75781 | -3 | 28.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.892 | 1.93 | 99.9 | 0.585 | 0.585 | 2.7 | 3.9 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1OM4 | 1.892 | 32.24 | 71966 | 3761 | 98.86 | 0.18164 | 0.18004 | 0.21182 | RANDOM | 37.158 |
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] | |
0.14 | 0.06 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.251 |
r_dihedral_angle_4_deg | 17.005 |
r_dihedral_angle_3_deg | 14.279 |
r_dihedral_angle_1_deg | 5.798 |
r_scangle_it | 3.657 |
r_scbond_it | 2.301 |
r_angle_refined_deg | 1.417 |
r_mcangle_it | 1.364 |
r_mcbond_it | 0.755 |
r_chiral_restr | 0.102 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6646 |
Nucleic Acid Atoms | |
Solvent Atoms | 462 |
Heterogen Atoms | 177 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |