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The 0.95 A structure of an oxidoreductase, yciK from E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F1K 3F1K, ycik structure at 2.6A resolution, solved by MAD and SAD phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1M HEPES pH 7.5, 0.1M sodium nitrate, 16 % w/v polyethylene glycol 8000, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.98 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.871 α = 90 b = 66.803 β = 109.03 c = 65.053 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 MAR CCD 300 mm Si(III) Monochromator 2007-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9184 APS 21-ID-D
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 0.95 45.24 86.7 0.062 8.9 4.44 236813 8.3
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) 0.95 0.98 80.9 0.385 2.8 4.54 22049
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3F1K, ycik structure at 2.6A resolution, solved by MAD and SAD phasing 0.95 34.136 236747 1830 86.65 0.171 0.171 0.1658 0.192 0.1861 RANDOM 18.207
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] -0.568 0.425 -0.205 0.772
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.72 f_angle_d 0.915 f_chiral_restr 0.073 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7611 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms
Software Software Software Name Purpose d*TREK data processing PHENIX refinement PDB_EXTRACT data extraction d*TREK data scaling PHENIX phasing