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Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (NP_812074.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2000M NaOAc, 30.0000% PEG-8000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.223 α = 90 b = 76.978 β = 90 c = 132.8 γ = 90
Symmetry Space Group C 2 2 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) 2009-03-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97993,0.97920 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 1.35 29.05 100 0.085 0.085 9.7 3.6 61313 10.639
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 1.35 1.39 100 0.59 0.59 1.9 3.1 4503
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 1.35 29.05 61269 3109 99.96 0.151 0.15 0.1516 0.172 0.1726 RANDOM 10.685
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] -0.09 0.17 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 18.009 r_dihedral_angle_3_deg 10.233 r_dihedral_angle_1_deg 4.476 r_scangle_it 3.598 r_scbond_it 2.287 r_angle_refined_deg 1.71 r_mcangle_it 1.386 r_angle_other_deg 1.199 r_mcbond_it 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 18.009 r_dihedral_angle_3_deg 10.233 r_dihedral_angle_1_deg 4.476 r_scangle_it 3.598 r_scbond_it 2.287 r_angle_refined_deg 1.71 r_mcangle_it 1.386 r_angle_other_deg 1.199 r_mcbond_it 0.809 r_mcbond_other 0.236 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2218 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing