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Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.49 64.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.153 α = 90 b = 84.153 β = 90 c = 214.882 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-04-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97855,0.97783 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.05 30.069 99.4 0.08 11.54 7 49371 -3 34.435
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.12 95.9 0.971 1.4
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 2.05 30.069 49285 2492 99.69 0.214 0.212 0.2178 0.244 0.2471 RANDOM 46.781
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] 0.05 0.05 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.211 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 11.941 r_scangle_it 5.753 r_dihedral_angle_1_deg 4.78 r_scbond_it 4.579 r_mcangle_it 2.791 r_mcbond_it 2.073 r_angle_refined_deg 1.515 r_angle_other_deg 1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.211 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 11.941 r_scangle_it 5.753 r_dihedral_angle_1_deg 4.78 r_scbond_it 4.579 r_mcangle_it 2.791 r_mcbond_it 2.073 r_angle_refined_deg 1.515 r_angle_other_deg 1.184 r_mcbond_other 1.022 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.166 r_nbd_other 0.162 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_other 0.146 r_symmetry_vdw_refined 0.143 r_nbtor_other 0.084 r_chiral_restr 0.072 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3824 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHARP phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction