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Crystal structure of probable 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE ABAYE1769 (TARGET EFI-505029) from Acinetobacter baumannii with citric acid bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FFI PDB entry 2FFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 0.1M SODIUM HYDROGEN PHOSPHATE: CITRIC ACID, PH 4.2, 40% ETHANOL, 5% PEG 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.168 α = 90 b = 75.168 β = 90 c = 88.966 γ = 120
Symmetry Space Group P 31 2 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 2011-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.276 50 96.2 0.108 7.4 6.6 13753 -5 45.27
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 2.276 2.31 99.7 0.97 2 6.7
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 MR THROUGHOUT PDB entry 2FFI 2.276 34.62 12783 417 96.01 0.21518 0.21316 0.2015 0.28041 0.2807 RANDOM 53.519
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] -0.73 -0.37 -0.73 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 19.843 r_dihedral_angle_3_deg 16.025 r_scangle_it 10.797 r_scbond_it 8.435 r_mcangle_it 6.401 r_dihedral_angle_1_deg 5.426 r_mcbond_it 4.786 r_angle_refined_deg 1.057 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 19.843 r_dihedral_angle_3_deg 16.025 r_scangle_it 10.797 r_scbond_it 8.435 r_mcangle_it 6.401 r_dihedral_angle_1_deg 5.426 r_mcbond_it 4.786 r_angle_refined_deg 1.057 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 13
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling