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Crystal Structure of yciK from E. coli, an oxidoreductase, complexed with NADP+ at 2.6A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 0.1M Sodium Acetate monohydrate pH 4.6, 8% w/v polyethylene glycol 4000, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.509 α = 90 b = 88.509 β = 90 c = 80.419 γ = 120
Symmetry Space Group P 32 2 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 2007-11-01 M MAD 2 1 x-ray 100 CCD MAR CCD 165 mm Diamond (III) Monochromator 2007-11-23 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97887, 0.97864, 0.96860 APS 21-ID-D 2 SYNCHROTRON APS BEAMLINE 31-ID 0.97990 APS 31-ID
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 2.5 44.25 99.9 0.114 16.6 21.76 12975 53.3
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) 2.5 2.59 100 0.424 6.3 21.4 1282
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION MAD, SAD 2.6 35.608 21570 2188 99.62 0.216 0.211 0.2098 0.261 0.2557 58.194
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] -3.711 -3.711 7.423
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.705 f_angle_d 1.416 f_chiral_restr 0.082 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1956 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data processing PHENIX refinement PDB_EXTRACT data extraction d*TREK data reduction d*TREK data scaling PHENIX phasing