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Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 0.2000M KCl, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.29 α = 90 b = 80.29 β = 90 c = 145.02 γ = 120
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 2008-08-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97929,0.97915 SSRL BL9-2
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 1.75 26.764 99.2 0.06 12.89 5.5 18394 -3 21.006
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 1.75 1.81 97.1 0.577 1.9
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 1.75 26.764 18393 939 99.82 0.17 0.168 0.1729 0.205 0.2095 RANDOM 23.605
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] -0.67 -0.33 -0.67 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.152 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_1_deg 5.994 r_scangle_it 5.655 r_scbond_it 4.283 r_mcangle_it 3.462 r_mcbond_it 2.733 r_angle_refined_deg 1.046 r_angle_other_deg 0.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.152 r_dihedral_angle_4_deg 16.352 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_1_deg 5.994 r_scangle_it 5.655 r_scbond_it 4.283 r_mcangle_it 3.462 r_mcbond_it 2.733 r_angle_refined_deg 1.046 r_angle_other_deg 0.697 r_mcbond_other 0.687 r_symmetry_vdw_other 0.276 r_nbd_other 0.218 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.201 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.104 r_chiral_restr 0.086 r_nbtor_other 0.084 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_symmetry_hbond_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1170 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing