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Crystal structure of the complex of phospho pantetheine adenylyl transferase from Acinetobacter baumannii with two ascorbic acid (Vitamin-C) molecules.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6
Crystal Properties Matthews coefficient Solvent content 5.73 78.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.667 α = 90 b = 216.667 β = 90 c = 216.667 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 PSI PILATUS 6M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97199 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.3 125.1 100 0.12 0.96 14.65 20 19945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 100 1.3 0.82 3.76
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 5ZZC 2.3 125.09 18920 1025 100 0.19466 0.19305 0.1976 0.22572 0.2321 RANDOM 53.199
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 30.615 r_dihedral_angle_4_deg 21.306 r_dihedral_angle_3_deg 20.031 r_long_range_B_other 13.56 r_long_range_B_refined 13.556 r_scangle_other 11.756 r_scbond_it 8.645 r_scbond_other 8.467 r_mcangle_other 7.807 r_mcangle_it 7.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.615 r_dihedral_angle_4_deg 21.306 r_dihedral_angle_3_deg 20.031 r_long_range_B_other 13.56 r_long_range_B_refined 13.556 r_scangle_other 11.756 r_scbond_it 8.645 r_scbond_other 8.467 r_mcangle_other 7.807 r_mcangle_it 7.791 r_dihedral_angle_1_deg 6.646 r_mcbond_it 5.74 r_mcbond_other 5.654 r_angle_refined_deg 2.22 r_angle_other_deg 1.448 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 1305 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building REFMAC phasing