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Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with 2-hydroxy-1,2,3-propane tricarboxylate at 1.76 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M HEPES Na pH 7.5, 1.0M Na citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.3 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.262 α = 90 b = 109.389 β = 90 c = 121.275 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 MARRESEARCH MIRROR 2016-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 1.76 40.61 99.7 0.138 10.5 5.4 103655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 95.5 3.2
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 1H1T 1.76 40.61 102125 1118 99.59 0.20978 0.20928 0.2175 0.25634 0.2647 RANDOM 40.484
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] -0.02 -0.32 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.393 r_dihedral_angle_4_deg 22.86 r_dihedral_angle_3_deg 15.748 r_long_range_B_other 10.86 r_long_range_B_refined 10.857 r_scangle_other 7.396 r_dihedral_angle_1_deg 6.142 r_mcangle_other 5.787 r_mcangle_it 5.786 r_scbond_it 4.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.393 r_dihedral_angle_4_deg 22.86 r_dihedral_angle_3_deg 15.748 r_long_range_B_other 10.86 r_long_range_B_refined 10.857 r_scangle_other 7.396 r_dihedral_angle_1_deg 6.142 r_mcangle_other 5.787 r_mcangle_it 5.786 r_scbond_it 4.797 r_scbond_other 4.797 r_mcbond_it 3.778 r_mcbond_other 3.772 r_angle_refined_deg 1.959 r_angle_other_deg 1.045 r_chiral_restr 0.213 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 7944 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing