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Crystal structure of the complex of Phosphopantetheine adenylyltransferasefrom Acinetobacter baumannii with Ascorbic acid (Vitamin-C) at 2.0A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, pH 5.6
Crystal Properties Matthews coefficient Solvent content 5.74 78.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.71 α = 90 b = 216.71 β = 90 c = 216.71 γ = 90
Symmetry Space Group F 41 3 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 PIXEL DECTRIS PILATUS 2M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97119 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2 125.12 97.7 0.04 10.9 20 29100
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 68.6 0.886
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 6J3M 2 125.12 27673 1428 97.62 0.19954 0.19877 0.2085 0.21506 0.2218 RANDOM 53.657
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.795 r_dihedral_angle_3_deg 21.728 r_dihedral_angle_4_deg 21.507 r_long_range_B_refined 18.378 r_long_range_B_other 18.116 r_scangle_other 12.169 r_scbond_it 9.088 r_scbond_other 8.839 r_mcangle_it 7.454 r_mcangle_other 7.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.795 r_dihedral_angle_3_deg 21.728 r_dihedral_angle_4_deg 21.507 r_long_range_B_refined 18.378 r_long_range_B_other 18.116 r_scangle_other 12.169 r_scbond_it 9.088 r_scbond_other 8.839 r_mcangle_it 7.454 r_mcangle_other 7.45 r_dihedral_angle_1_deg 6.669 r_mcbond_it 5.668 r_mcbond_other 5.625 r_angle_refined_deg 2.325 r_angle_other_deg 1.534 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 1305 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building