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Crystal structure of nitrate/nitrite exchanger NarK with nitrite bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JR9 PDB ENTRY 4JR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 277 28% PEG400, 0.1 M citric acid pH 3.5, 0.1M NaCl and 0.1M Li2SO4. The crystal was subsequently soaked with 50mM NaNO2 in the above solution prior to freezing, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.14 70.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.91 α = 100.07 b = 81.407 β = 96.38 c = 138.487 γ = 115.92
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 2012-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.99999 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 94.6 0.158 7.9 3.6 72283 1.1 57.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 76.3 0.866 1.1 2.9 2893
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4JR9 2.8 50 72136 68494 3642 94.53 0.22567 0.22337 0.2234 0.2686 0.266 RANDOM 57.172
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] -0.68 -0.23 -1.11 -0.1 1.65 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.015 r_dihedral_angle_3_deg 20.783 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_1_deg 6.018 r_angle_refined_deg 1.29 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12522 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 32
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling