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Structure of neuronal nitric oxide synthase heme domain in complex with 6,6'-(2,2'-(pyridine-3,5-diyl)bis(ethane-2,1-diyl))bis(4-methylpyridin-2-amine)
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 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.34 α = 90 b = 111.21 β = 90 c = 164.82 γ = 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 ADSC QUANTUM 315 mirror 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.976 SSRL BL7-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.73 50 99.5 0.051 0.051 29.1 4 101279 -3 25.5
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) 1.73 1.76 99.8 0.59 0.59 2.1 4
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1OM4 1.73 38.11 95347 5018 99.15 0.18314 0.18197 0.1922 0.2053 0.2188 RANDOM 33.563
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] 0.11 0.15 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.235 r_dihedral_angle_4_deg 16.645 r_dihedral_angle_3_deg 13.549 r_dihedral_angle_1_deg 5.461 r_scangle_it 3.146 r_scbond_it 1.945 r_angle_refined_deg 1.241 r_mcangle_it 1.22 r_mcbond_it 0.648 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.235 r_dihedral_angle_4_deg 16.645 r_dihedral_angle_3_deg 13.549 r_dihedral_angle_1_deg 5.461 r_scangle_it 3.146 r_scbond_it 1.945 r_angle_refined_deg 1.241 r_mcangle_it 1.22 r_mcbond_it 0.648 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 6658 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement CNS refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing