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Crystal structure of a putative gamma-carboxymuconolactone decarboxylase subunit (bxe_b0980) from burkholderia xenovorans lb400 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 20.0% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.3 α = 90 b = 83.11 β = 103.16 c = 99.26 γ = 90
Symmetry Space Group P 1 21 1
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) 2007-05-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97941, 0.97905 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 1.7 29.086 95 0.074 6.95 86578 -3 16.23
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) 1 1.7 1.76 93.6 0.492 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 1.7 29.086 86554 4333 98.99 0.156 0.154 0.1615 0.193 0.1967 RANDOM 13.832
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 0.3 0.18 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.085 r_dihedral_angle_4_deg 16.522 r_dihedral_angle_3_deg 12.462 r_scangle_it 6.327 r_dihedral_angle_1_deg 4.988 r_scbond_it 4.525 r_mcangle_it 2.575 r_mcbond_it 2.115 r_angle_refined_deg 1.509 r_angle_other_deg 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.085 r_dihedral_angle_4_deg 16.522 r_dihedral_angle_3_deg 12.462 r_scangle_it 6.327 r_dihedral_angle_1_deg 4.988 r_scbond_it 4.525 r_mcangle_it 2.575 r_mcbond_it 2.115 r_angle_refined_deg 1.509 r_angle_other_deg 1.07 r_mcbond_other 0.57 r_nbd_refined 0.225 r_nbd_other 0.195 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.094 r_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5908 Nucleic Acid Atoms Solvent Atoms 943 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing SOLVE phasing