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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 Na Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.9 79.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.274 α = 90 b = 164.274 β = 90 c = 164.274 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 1.28269 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 2.9 50 100 0.077 32.2 12.5 32293 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 2.9 3.08 100 0.436 11.2 5342
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 2.92 50 32828 30501 1632 99.64 0.16365 0.16201 0.1626 0.19495 0.191 RANDOM 76.63
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 37.043 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 16.202 r_dihedral_angle_1_deg 7.136 r_scangle_it 2.344 r_scbond_it 1.492 r_angle_refined_deg 1.354 r_mcangle_it 0.802 r_mcbond_it 0.529 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.043 r_dihedral_angle_3_deg 19.074 r_dihedral_angle_4_deg 16.202 r_dihedral_angle_1_deg 7.136 r_scangle_it 2.344 r_scbond_it 1.492 r_angle_refined_deg 1.354 r_mcangle_it 0.802 r_mcbond_it 0.529 r_nbtor_refined 0.309 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.207 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_metal_ion_refined 0.009 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_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 4268 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MLPHARE phasing