4LUX

Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OM4PDB ENTRY 1OM4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.827820-22% PEG3350, 0.1 M MES, 0.2 M ammonium acetate, 10% ethylene glycol, 30 uM SDS, 5 mM GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.839α = 90
b = 110.887β = 90
c = 164.681γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2011-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.100SSRLBL7-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.865099.60.0660.06624.2480574-328.1
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)RedundancyNumber Unique Reflections (All)
11.861.8998.80.5810.5811.74

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1OM41.8639.0180292396299.230.181570.179960.21232RANDOM39.721
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]
0.160.08-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.006
r_dihedral_angle_4_deg17.903
r_dihedral_angle_3_deg15.382
r_dihedral_angle_1_deg5.845
r_scangle_it3.352
r_scbond_it2.137
r_angle_refined_deg1.42
r_mcangle_it1.304
r_mcbond_it0.728
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.006
r_dihedral_angle_4_deg17.903
r_dihedral_angle_3_deg15.382
r_dihedral_angle_1_deg5.845
r_scangle_it3.352
r_scbond_it2.137
r_angle_refined_deg1.42
r_mcangle_it1.304
r_mcbond_it0.728
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6658
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms181

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing