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Structure of rat nitric oxide synthase heme domain in complex with 4-methyl-6-(((3R,4R)-4-((5-(pyridin-2-yl)pentyl)oxy)pyrrolidin-3-yl)methyl)pyridin-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, 0.1M MES, 140-200mM Ammonium Sulfate, 10% Ethylene Glycol, 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.079 α = 90 b = 110.801 β = 90 c = 164.412 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 mirrors 2010-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 ALS 8.2.2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.886 50 97.2 0.056 0.056 22.7 4.1 75429 -3 30
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 1.886 1.92 96.8 0.546 0.546 1.9 4.2
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 1.886 49.89 71429 3761 96.9 0.17657 0.17485 0.1926 0.2088 0.2255 RANDOM 43.991
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] 0.67 1.27 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.815 r_scangle_it 3.621 r_scbond_it 2.3 r_angle_refined_deg 1.421 r_mcangle_it 1.412 r_mcbond_it 0.777 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.07 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 14.602 r_dihedral_angle_1_deg 5.815 r_scangle_it 3.621 r_scbond_it 2.3 r_angle_refined_deg 1.421 r_mcangle_it 1.412 r_mcbond_it 0.777 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 367 Heterogen Atoms 181
Software Software Software Name Purpose BOS data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing