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Crystal structure of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3I PDB ENTRY 1T3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.5 278 20% PEG3000, 0.2M sodium chloride and 0.1M HEPES pH 7.5, microbatch under oil, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.567 α = 90 b = 68.205 β = 94.76 c = 87.066 γ = 90
Symmetry Space Group P 1 21 1
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 2012-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.978542 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.709 45.853 95 97828 97823
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 1.71 1.8 75 0.187 3.5 2.6 11087
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1T3I 1.709 45.853 1.34 97828 97823 4892 94.77 0.204 0.204 0.2025 0.2002 0.2326 0.2294 Scaling input intensities via French-Wilson Method
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] -0.8666 -0.7462 -0.4169 1.2835
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.085 f_angle_d 1.127 f_chiral_restr 0.076 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6444 Nucleic Acid Atoms Solvent Atoms 854 Heterogen Atoms
Software Software Software Name Purpose Xnemo data collection MOLREP phasing PHENIX refinement XDS data reduction SCALA data scaling