3UFW
Structure of rat nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-((5-(6-aminopyridin-2-yl)pentyl)oxy)pyrrolidin-3-yl)methyl)-4-methylpyridin-2-amine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1OM4 | PDB ENTRY 1OM4 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | 277 | 20-24% PEG3350, 0.1M MES, 140-200mM Ammonium Sulfate, 10% Ethylene Glycol, 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.43 | 49.3 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 51.902 | ¦Á = 90 |
b = 111.245 | ¦Â = 90 |
c = 164.084 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | P 21 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 | 100 | CCD | ADSC QUANTUM 315 | mirrors | 2011-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 1.097 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 50 | 99.4 | 0.077 | 0.077 | 24.5 | 4 | 64761 | -3 | 35.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 2.03 | 99.9 | 0.654 | 0.654 | 1.6 | 3.9 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1OM4 | 2 | 38.49 | 61504 | 3186 | 99.34 | 0.19845 | 0.19603 | 0.24444 | RANDOM | 54.351 |
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] | |
0.36 | 0.19 | -0.54 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.617 |
r_dihedral_angle_4_deg | 17.774 |
r_dihedral_angle_3_deg | 15.505 |
r_dihedral_angle_1_deg | 6.181 |
r_scangle_it | 3.3 |
r_scbond_it | 2.253 |
r_angle_refined_deg | 1.513 |
r_mcangle_it | 1.312 |
r_mcbond_it | 0.746 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6658 |
Nucleic Acid Atoms | |
Solvent Atoms | 252 |
Heterogen Atoms | 183 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |