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CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288) FROM POLAROMONAS SP. JS666 WITH BOUND MANGANESE AND AN INHIBITOR, 2-NITRORESORCINOL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.1M SODIUM ACETATE, PH 4.6, 1M AMMONIUM CITRATE DIBASIC, 5MM MANGANESE CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.73 54.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.958 α = 90 b = 151.058 β = 92.15 c = 143.826 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 ADSC QUANTUM 315 MIRRORS 2014-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 50 99.8 0.098 0.098 12.4 3.9 412849 -5
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 1.68 99.8 0.67 0.67 1.5 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3S4T 1.65 50 399829 12420 99.77 0.1902 0.18917 0.2026 0.22344 0.2343 RANDOM 35.361
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] -1.45 0.26 -1.99 3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.335 r_dihedral_angle_4_deg 18.469 r_scbond_it 14.828 r_scbond_other 14.761 r_scangle_other 13.003 r_dihedral_angle_3_deg 12.609 r_long_range_B_refined 12.175 r_long_range_B_other 12.174 r_dihedral_angle_1_deg 6.789 r_mcbond_it 6.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.335 r_dihedral_angle_4_deg 18.469 r_scbond_it 14.828 r_scbond_other 14.761 r_scangle_other 13.003 r_dihedral_angle_3_deg 12.609 r_long_range_B_refined 12.175 r_long_range_B_other 12.174 r_dihedral_angle_1_deg 6.789 r_mcbond_it 6.668 r_mcbond_other 6.637 r_mcangle_other 6.408 r_mcangle_it 6.406 r_angle_refined_deg 1.476 r_angle_other_deg 0.83 r_chiral_restr 0.124 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21059 Nucleic Acid Atoms Solvent Atoms 2241 Heterogen Atoms 180
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling