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Glycerophosphodiesterase from Enterobacter aerogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 1.9M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.9 79.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.462 α = 90 b = 164.462 β = 90 c = 164.462 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 2006-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 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 3 50 100 0.073 34.3 14 29959 77.2
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 3 3.19 100 0.424 4.6 12.3 4934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 3 50 29917 28390 1527 99.9 0.15984 0.15805 0.1594 0.19384 0.1932 RANDOM 72.749
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 36.237 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 19.112 r_dihedral_angle_1_deg 7.2 r_scangle_it 2.155 r_angle_refined_deg 1.356 r_scbond_it 1.352 r_mcangle_it 0.724 r_mcbond_it 0.569 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.237 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 19.112 r_dihedral_angle_1_deg 7.2 r_scangle_it 2.155 r_angle_refined_deg 1.356 r_scbond_it 1.352 r_mcangle_it 0.724 r_mcbond_it 0.569 r_nbtor_refined 0.312 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.126 r_xyhbond_nbd_refined 0.12 r_symmetry_vdw_refined 0.114 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 4274 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SHELXS phasing