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Structure of neuronal nitric oxide synthase heme domain in complex with 6,6'-(2,2'-(pyridine-2,6-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 277.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.71 α = 90 b = 110.61 β = 90 c = 164.08 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 2008-11-30 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 2.05 50 99.4 0.066 0.066 21.2 4 60097 -3 31.2
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) 2.05 2.09 94.6 0.564 0.564 1.9 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1OM4 2.05 43.73 56712 2938 99.4 0.18609 0.18395 0.22797 0.2217 RANDOM 43.433
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] -0.18 -0.09 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 5.713 r_scangle_it 3.062 r_scbond_it 1.922 r_angle_refined_deg 1.316 r_mcangle_it 1.111 r_mcbond_it 0.591 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 14.882 r_dihedral_angle_1_deg 5.713 r_scangle_it 3.062 r_scbond_it 1.922 r_angle_refined_deg 1.316 r_mcangle_it 1.111 r_mcbond_it 0.591 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 358 Heterogen Atoms 181
Software Software Software Name Purpose REFMAC refinement CNS refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing