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Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JOG
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 5.64 78.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.539 α = 90 b = 215.539 β = 90 c = 215.539 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 CCD MARMOSAIC 225 mm CCD 2019-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 1 RRCAT INDUS-2 PX-BL21
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 3.2 49.5 92.27 0.117 0.98 30.61 8.5 6957
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 3.2 3.28 0.7 0.92 5.02 13
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6JOG 3.202 49.497 6957 334 92.378 0.178 0.175 0.1776 0.2327 0.2203 76.279
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 29.545 r_dihedral_angle_4_deg 23.835 r_dihedral_angle_3_deg 20.833 r_lrange_other 17.225 r_lrange_it 17.222 r_scangle_it 13.69 r_scangle_other 13.683 r_mcangle_it 11.489 r_mcangle_other 11.485 r_scbond_it 9.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.545 r_dihedral_angle_4_deg 23.835 r_dihedral_angle_3_deg 20.833 r_lrange_other 17.225 r_lrange_it 17.222 r_scangle_it 13.69 r_scangle_other 13.683 r_mcangle_it 11.489 r_mcangle_other 11.485 r_scbond_it 9.2 r_scbond_other 9.194 r_dihedral_angle_1_deg 8.41 r_mcbond_it 7.499 r_mcbond_other 7.461 r_angle_refined_deg 1.821 r_angle_other_deg 1.317 r_nbd_other 0.3 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.23 r_symmetry_nbd_other 0.219 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_refined 0.075 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1305 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing