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Crystal structure of an H-NOX protein from S. oneidensis in the Fe(II)NO ligation state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Obtained by equilibrating a 2 or 4 uL drop of 1:1 protein: reservoir against 700 uL reservoir containing 0.7 M NaH2PO4, 0.9 M K2HPO4. Cryoprotection was achieved by carefully adding equal drop volume of mother liquor containing 50% glycerol. Crystals were then transferred into mother liquor containing 30% glycerol and flash frozen in liquid nitrogen. All crystal growth and manipulation was performed anaerobically.
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.636 α = 90 b = 86.716 β = 90 c = 33.822 γ = 90
Symmetry Space Group P 21 21 2
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 315r 2012-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.11 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 33.818 98.46 0.029 14.4 3.9 45550 45550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 99.5 0.487 1.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4U99 1.65 33.818 1.33 45550 2302 98.46 0.1693 0.1675 0.1747 0.2027 0.2109
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.749 f_angle_d 0.864 f_chiral_restr 0.029 f_bond_d 0.019 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1430 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement