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Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.57 277 NANODROP, 23.4% PEG 4000, 15.0% Glycerol, 0.17M Ammonium acetate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.173 α = 90 b = 71.173 β = 90 c = 325.501 γ = 120
Symmetry Space Group P 61 2 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 collimating mirror, toroid focusing mirror 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97903, 0.97920 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 1.65 29.761 100 0.147 0.147 13.8 10.6 60310 17.94
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 1.65 1.69 100 0.012 1.24 2 10.8 4353
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 1.65 29.761 60156 3039 99.97 0.154 0.152 0.161 0.18 0.1853 RANDOM 9.037
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] 0.51 0.25 0.51 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.898 r_dihedral_angle_4_deg 15.408 r_dihedral_angle_3_deg 11.702 r_scangle_it 7.126 r_dihedral_angle_1_deg 5.428 r_scbond_it 4.947 r_mcangle_it 2.477 r_mcbond_it 1.873 r_angle_refined_deg 1.764 r_angle_other_deg 1.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.898 r_dihedral_angle_4_deg 15.408 r_dihedral_angle_3_deg 11.702 r_scangle_it 7.126 r_dihedral_angle_1_deg 5.428 r_scbond_it 4.947 r_mcangle_it 2.477 r_mcbond_it 1.873 r_angle_refined_deg 1.764 r_angle_other_deg 1.054 r_mcbond_other 0.511 r_symmetry_vdw_refined 0.353 r_symmetry_vdw_other 0.28 r_nbd_refined 0.235 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.19 r_nbtor_refined 0.182 r_chiral_restr 0.1 r_nbtor_other 0.085 r_xyhbond_nbd_other 0.059 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 91
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 SOLVE phasing