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Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 35.0000% 2-propanol, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.427 α = 90 b = 99.797 β = 90 c = 134.656 γ = 90
Symmetry Space Group P 21 21 21
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) 2009-06-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97951,0.97870 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 29.828 100 0.086 0.086 11.1 4.1 104654 20.364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.85 100 0.662 0.662 2 4.1 7685
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 1.8 29.828 104578 5227 99.96 0.168 0.166 0.1724 0.205 0.2095 RANDOM 26.606
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] 0.33 0.94 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 11.919 r_scangle_it 5.682 r_dihedral_angle_1_deg 4.744 r_scbond_it 4.464 r_mcangle_it 2.68 r_mcbond_it 2.039 r_angle_refined_deg 1.438 r_angle_other_deg 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 11.919 r_scangle_it 5.682 r_dihedral_angle_1_deg 4.744 r_scbond_it 4.464 r_mcangle_it 2.68 r_mcbond_it 2.039 r_angle_refined_deg 1.438 r_angle_other_deg 1.05 r_mcbond_other 0.574 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.186 r_nbd_other 0.185 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.171 r_symmetry_vdw_refined 0.104 r_nbtor_other 0.088 r_chiral_restr 0.086 r_metal_ion_refined 0.024 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7749 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction