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Crystal structure of the beta subunit of the benzoate 1,2-dioxygenase (benb, bmaa0186) from burkholderia mallei atcc 23344 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 15.0000% Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.17 43.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.953 α = 90 b = 58.953 β = 90 c = 167.073 γ = 120
Symmetry Space Group P 63 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 mirror (vertical focusing) 2008-07-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97822,0.97901 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 1.9 29.476 99.6 0.073 7.03 5.2 14285 26.262
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.509 0.509 0.568 1.4 5.3 1022
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 1.9 29.476 14242 717 99.17 0.188 0.186 0.1897 0.223 0.232 RANDOM 30.839
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.707 r_dihedral_angle_4_deg 15.907 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 6.342 r_scangle_it 5.892 r_scbond_it 4.966 r_mcangle_it 3.099 r_mcbond_it 2.095 r_angle_refined_deg 1.46 r_angle_other_deg 0.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.707 r_dihedral_angle_4_deg 15.907 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 6.342 r_scangle_it 5.892 r_scbond_it 4.966 r_mcangle_it 3.099 r_mcbond_it 2.095 r_angle_refined_deg 1.46 r_angle_other_deg 0.911 r_mcbond_other 0.566 r_symmetry_vdw_other 0.281 r_symmetry_hbond_refined 0.222 r_nbd_other 0.219 r_nbd_refined 0.199 r_nbtor_refined 0.192 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.093 r_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction