3NLP

Structure of neuronal nitric oxide synthase D597N/M336V mutant heme domain in complex with 6-{{(3'S,4'S)-3'-[2"-(3'''-fluorophenethylamino)ethoxy]pyrrolidin-4'-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 DROP5.827720-24% PEG3350, 100mM MES, 100-140mM ammonium acetate, 5mM GSH, 35uM SDS , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.763α = 90
b = 110.996β = 90
c = 164.632γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirror2007-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.000SSRLBL9-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.025098.80.0490.049283.962123-335.6
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)
2.022.0797.10.6890.6892.33.5

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 1OM42.0238.659003307998.560.188620.186550.22785RANDOM56.968
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]
4.49-0.65-3.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg16.045
r_dihedral_angle_1_deg5.987
r_scangle_it3.454
r_scbond_it2.263
r_angle_refined_deg1.534
r_mcangle_it1.381
r_mcbond_it0.796
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.118
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg16.045
r_dihedral_angle_1_deg5.987
r_scangle_it3.454
r_scbond_it2.263
r_angle_refined_deg1.534
r_mcangle_it1.381
r_mcbond_it0.796
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms6656
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms195

Software

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