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Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EY9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 286 0.1M MES/NaOH, 20-35% 2-methyl-2,4-pentanediol (MPD), pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.243 α = 90 b = 207.051 β = 90 c = 214.542 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD mirrors 2007-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
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 2.5 84.82 99.6 0.132 0.132 4.722 5.2 309368 52.76
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) 2.5 2.64 98.4 0.704 0.704 1.1 4.6 44197
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3EY9 2.5 30 308673 308673 15217 99.62 0.184 0.184 0.183 0.1857 0.198 0.1856 RANDOM 63.922
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] 1.73 -1.08 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 22.895 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 5.596 r_scangle_it 2.072 r_mcangle_it 1.723 r_angle_refined_deg 1.467 r_scbond_it 1.298 r_mcbond_it 0.944 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_4_deg 22.895 r_dihedral_angle_3_deg 17.179 r_dihedral_angle_1_deg 5.596 r_scangle_it 2.072 r_mcangle_it 1.723 r_angle_refined_deg 1.467 r_scbond_it 1.298 r_mcbond_it 0.944 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47891 Nucleic Acid Atoms Solvent Atoms 1329 Heterogen Atoms 1140
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection