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Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.6 277 40% (v/v) PEG-600, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 9.60
Crystal Properties Matthews coefficient Solvent content 2.22 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.41 α = 90 b = 41.79 β = 90 c = 51.72 γ = 90
Symmetry Space Group P 21 21 2
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 APS-1 water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2002-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98011, 0.97938, 0.97918, 0.95671 APS 19-BM
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 1.6 50 100 0.05 62.01 6.71 38012
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 1.6 1.66 95.3 0.196 10.06 3.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.6 48.18 36027 1926 97.8 0.141 0.139 0.1525 0.18 0.1942 RANDOM 13.32
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] 0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_4_deg 19.046 r_dihedral_angle_3_deg 10.828 r_scangle_it 6.905 r_dihedral_angle_1_deg 6.079 r_scbond_it 4.411 r_mcangle_it 3.054 r_mcbond_it 1.79 r_angle_refined_deg 1.411 r_angle_other_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_4_deg 19.046 r_dihedral_angle_3_deg 10.828 r_scangle_it 6.905 r_dihedral_angle_1_deg 6.079 r_scbond_it 4.411 r_mcangle_it 3.054 r_mcbond_it 1.79 r_angle_refined_deg 1.411 r_angle_other_deg 0.882 r_symmetry_vdw_other 0.336 r_symmetry_vdw_refined 0.306 r_symmetry_hbond_refined 0.244 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.23 r_nbd_refined 0.211 r_metal_ion_refined 0.115 r_chiral_restr 0.091 r_nbtor_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1831 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling RESOLVE model building SOLVE phasing ARP/wARP model building REFMAC refinement RESOLVE phasing