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Crystal structure of 4-hydroxybutyrate CoA-transferase (abfT-2) from Porphyromonas gingivalis. Northeast Structural Genomics Consortium target PgR26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Acetyl-CoA. Reservoir solution: 200 mM Ammonium citrate pH 5.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.684 α = 90 b = 87.279 β = 90 c = 93.504 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm Mirrors 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97900 NSLS X4C
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 2.8 29.35 99.8 0.112 0.097 12.43 3.2 21251 21251 28.5
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 2.8 2.9 100 0.354 0.324 2.25 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.8 29.35 21251 10089 505 100 0.20172 0.19863 0.1996 0.25967 0.2599 RANDOM 24.309
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] 1.43 -1.98 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.745 r_dihedral_angle_3_deg 25.22 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_1_deg 7.975 r_scangle_it 5.599 r_scbond_it 3.575 r_angle_refined_deg 2.806 r_mcangle_it 2.075 r_mcbond_it 1.219 r_nbtor_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.745 r_dihedral_angle_3_deg 25.22 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_1_deg 7.975 r_scangle_it 5.599 r_scbond_it 3.575 r_angle_refined_deg 2.806 r_mcangle_it 2.075 r_mcbond_it 1.219 r_nbtor_refined 0.35 r_symmetry_vdw_refined 0.34 r_nbd_refined 0.299 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.177 r_symmetry_hbond_refined 0.121 r_bond_refined_d 0.033 r_gen_planes_refined 0.009 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_refined 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 3018 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SnB phasing SOLVE phasing RESOLVE phasing