3N60
Structure of neuronal nitric oxide synthase heme domain in complex with 6,6'-(2,2'-(5-amino-1,3-phenylene)bis(ethane-2,1-diyl))bis(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 100mM MES 100-140mM ammonium acetate 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.42 | 49.21 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 51.86 | ¦Á = 90 |
| b = 111.17 | ¦Â = 90 |
| c = 164.02 | ¦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 | MARMOSAIC 325 mm CCD | mirror | 2009-02-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 1.000 | SSRL | BL9-2 |
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 | 1.98 | 50 | 99.8 | 0.054 | 0.054 | 28.7 | 4.5 | 67020 | -3 | 34.2 | |||||||||
| 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) | ||||||||||
| 1.98 | 2.01 | 99.8 | 0.641 | 0.641 | 2.1 | 4.2 | |||||||||||||
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 | 1.98 | 37.63 | 63638 | 3286 | 99.81 | 0.19331 | 0.1913 | 0.23224 | RANDOM | 52.754 | ||||||
| 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] | |
| -0.21 | 0.21 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.239 |
| r_dihedral_angle_4_deg | 17.957 |
| r_dihedral_angle_3_deg | 15.504 |
| r_dihedral_angle_1_deg | 6.065 |
| r_scangle_it | 3.387 |
| r_scbond_it | 2.21 |
| r_angle_refined_deg | 1.476 |
| r_mcangle_it | 1.323 |
| r_mcbond_it | 0.746 |
| r_chiral_restr | 0.103 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6658 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 337 |
| Heterogen Atoms | 155 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CNS | refinement |
| Blu-Ice | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
