☰ Navigation Tabs
Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II) ligation state, Q154A/Q155A/K156A mutant
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 7.3 293 Obtained by equilibrating a 2 uL drop of 1:1 protein:reservoir against a 700 uL reservoir containing 1.6-1.9 M DL-malic acid (pH 7.3). For cryoprotection, 2 uL of mother liquor containing 10% glycerol was added directly to the drop and crystals were serial transferred into mother liquor solution containing 5, 7.5 and 10% glycerol prior to flash freezing in liquid nitrogen. Crystal growth and manipulation was performed anaerobically.
Crystal Properties Matthews coefficient Solvent content 4.56 73.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.801 α = 90 b = 163.801 β = 90 c = 102.082 γ = 120
Symmetry Space Group P 63 2 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 2013-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 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 2.1 48.027 96.52 0.032 12.8 4.8 86341 86341
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 2.1 2.16 98.6 0.655 1.1 2.4
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 2.1 48.027 1.33 86341 4389 96.52 0.1723 0.171 0.184 0.1972 0.2051
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 14.595 f_angle_d 1.65 f_chiral_restr 0.344 f_bond_d 0.021 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2951 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement