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Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DXN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 277 pH 7, VAPOR DIFFUSION, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.159 α = 90 b = 164.159 β = 90 c = 164.159 γ = 90
Symmetry Space Group P 21 3
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 ADSC QUANTUM 315 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.2947 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 30 98.2 0.069 20.9 73371 20.9 50.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.34 94.1 0.474 1.6 2.7 11622
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DXN 2.2 29.03 69628 3703 98.22 0.17059 0.16961 0.169 0.18906 0.1873 50.636
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.276 r_dihedral_angle_4_deg 21.713 r_dihedral_angle_3_deg 18.51 r_dihedral_angle_1_deg 6.785 r_scangle_it 3.492 r_scbond_it 2.288 r_angle_refined_deg 1.602 r_mcangle_it 1.239 r_mcbond_it 0.941 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.276 r_dihedral_angle_4_deg 21.713 r_dihedral_angle_3_deg 18.51 r_dihedral_angle_1_deg 6.785 r_scangle_it 3.492 r_scbond_it 2.288 r_angle_refined_deg 1.602 r_mcangle_it 1.239 r_mcbond_it 0.941 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.131 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4266 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing