3RQK
Structure of the neuronal nitric oxide synthase heme domain in complex with 4-methyl-6-{[(3R,4R)-4-(2-{[(1R,2S)-2-(3-methylphenyl)cyclopropyl]amino}ethoxy)pyrrolidin-3-yl]methyl}pyridin-2-amine and its isomer
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 | 278 | 22-24% PEG3350, 0.1M MES, 0.14M Ammonium acetate, 5mM GSH, 35uM SDS, 10% ethylene glycol, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.955 | α = 90 |
b = 111.529 | β = 90 |
c = 164.39 | 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 | ADSC QUANTUM 315 | mirrors | 2010-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 0.97946 | SSRL | BL7-1 |
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 | 2.2 | 50 | 97.9 | 0.076 | 0.076 | 25.6 | 3.8 | 47658 | -3 | 48.3 |
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 | 2.2 | 2.24 | 97.5 | 0.54 | 0.54 | 2.1 | 3.7 |
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 | 2.21 | 49.89 | 45045 | 2398 | 96.6 | 0.20352 | 0.20059 | 0.25782 | RANDOM | 64.517 |
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] | |
3.79 | 0.15 | -3.95 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.926 |
r_dihedral_angle_4_deg | 16.701 |
r_dihedral_angle_3_deg | 15.966 |
r_dihedral_angle_1_deg | 6.17 |
r_scangle_it | 3.185 |
r_scbond_it | 2.143 |
r_angle_refined_deg | 1.535 |
r_mcangle_it | 1.257 |
r_mcbond_it | 0.695 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6658 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms | 185 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |