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Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D40 PDB ENTRY 2D40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 12% w/v EtOH, 4% w/v PEG400, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.016 α = 90 b = 133.016 β = 90 c = 190.748 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE MAR scanner 345 mm plate 2005-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8423 EMBL/DESY, HAMBURG BW7B
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 2.9 109.109 99 0.154 0.154 4.3 4.8 38103 38103
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) 2.9 3.06 99.6 0.47 0.47 1.6 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2D40 2.9 20 37883 35989 1894 98.46 0.19656 0.19313 0.1973 0.26239 0.2615 RANDOM 42.108
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] -0.84 -0.84 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_4_deg 22.548 r_dihedral_angle_3_deg 21.232 r_dihedral_angle_1_deg 7.441 r_scangle_it 2.257 r_angle_refined_deg 1.714 r_scbond_it 1.4 r_mcangle_it 1.079 r_mcbond_it 0.609 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.922 r_dihedral_angle_4_deg 22.548 r_dihedral_angle_3_deg 21.232 r_dihedral_angle_1_deg 7.441 r_scangle_it 2.257 r_angle_refined_deg 1.714 r_scbond_it 1.4 r_mcangle_it 1.079 r_mcbond_it 0.609 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.269 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.114 r_metal_ion_refined 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10842 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 16
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction