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Crystal structure of the Phosphofructokinase-2 mutant Y23D from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CQD PDB entry 3CQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 291 23% PEG 4000, 0.1 M SODIUM ACETATE PH 4.75, 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.838 α = 90 b = 89.123 β = 90 c = 175.908 γ = 90
Symmetry Space Group P 2 2 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 2008-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.54 LNLS W01B-MX2
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 2.2 58.62 94.1 35587 33605 2 2 38.63
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 3CQD 2.2 48.98 1.35 35587 33560 1686 93.3 0.22 0.219 0.2169 0.253 0.2516 39.26
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] -1.5031 0.3302 3.0681
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.171 f_angle_d 0.927 f_chiral_restr 0.052 f_bond_d 0.012 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4436 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 84
Software Software Software Name Purpose PHASER phasing DM phasing PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction SCALA data scaling