3NLX

Structure of rat neuronal nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-(2- (2,2-Difluoro-2-(3-fluorophenyl)ethylamino)ethoxy)pyrrolidin-3-yl)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 DROP5.8277PEG 3350, MES, ammonium acetate, SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4649.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.301α = 90
b = 111.494β = 90
c = 164.413γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirrors2009-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-11.000SSRLBL11-1

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
11.875098.20.0530.05313.54.179054-327.65
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)
1.871.90.3590.3593.94.1

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 1OM41.8737.1675069393598.30.179570.1780.20922RANDOM36.471
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]
3.07-0.24-2.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.419
r_dihedral_angle_4_deg17.565
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.487
r_scangle_it3.117
r_scbond_it1.998
r_angle_refined_deg1.39
r_mcangle_it1.198
r_mcbond_it0.665
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.419
r_dihedral_angle_4_deg17.565
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.487
r_scangle_it3.117
r_scbond_it1.998
r_angle_refined_deg1.39
r_mcangle_it1.198
r_mcbond_it0.665
r_chiral_restr0.093
r_bond_refined_d0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6658
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms187

Software

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