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Crystal structure of the N-terminal truncated selenocysteine synthase SelA in complex with thiosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 120mM Tris-HCl, 12% PEG 4000, 800mM NaNO3, 160mM KCl, 50mM L-serine, 50mM Na2S2O3, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.442 α = 102.09 b = 116.372 β = 93.39 c = 124.788 γ = 106.06
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 mirrors 2007-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 3.25 50 99.3 0.129 0.129 12.7 3.9 76007 75475 -2
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 3.25 3.37 98.6 0.538 0.538 2.05 3.8
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 (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 3W1I 3.252 38.518 1.97 76178 75371 3812 98.94 0.2036 0.2003 0.1945 0.2661 0.259 RANDOM 123.2922
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] -40.2921 -0.5608 -7.5529 41.1022 -2.4413 -0.8101
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.109 f_angle_d 1.26 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30803 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 85
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling