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Crystal structure of putative thioesterase (YP_496845.1) from Novosphingobium aromaticivorans DSM 12444 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.19 293 NANODROP, 0.19M Calcium chloride, 19.6% PEG 400, 5.0% Glycerol, 0.1M HEPES pH 7.19, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.053 α = 90 b = 111.755 β = 90 c = 74.967 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 collimating mirror, toroid focusing mirror 2008-02-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97932, 0.97914 SSRL BL9-2
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 1.7 29.161 100 0.088 0.088 7 4 28153 17.089
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 1.7 1.74 100 0.636 0.636 1.2 4.1 2052
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 1.7 29.161 28130 1414 100 0.174 0.173 0.1782 0.203 0.2077 RANDOM 15.505
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] 1.31 -0.68 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.239 r_dihedral_angle_4_deg 14.416 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.256 r_scangle_it 3.722 r_scbond_it 2.406 r_angle_refined_deg 1.73 r_mcangle_it 1.605 r_angle_other_deg 1.186 r_mcbond_it 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.239 r_dihedral_angle_4_deg 14.416 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.256 r_scangle_it 3.722 r_scbond_it 2.406 r_angle_refined_deg 1.73 r_mcangle_it 1.605 r_angle_other_deg 1.186 r_mcbond_it 0.941 r_mcbond_other 0.254 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1823 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing