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Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 5-methoxy-2-methyl-1H-indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.8 M AMMONIUM SULFATE, 0.25 M POTASSIUM THIOCYANATE, 0.2 M POTASSIUM BROMIDE
Crystal Properties Matthews coefficient Solvent content 2.88 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.85 α = 90 b = 134.85 β = 90 c = 134.85 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.98 47.68 100 0.078 0.083 0.029 0.999 18.1 8 28483 23.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.03 100 0.443 0.475 0.169 0.908 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5JBN 1.981 28.75 1.03 28454 1448 99.97 0.1778 0.1768 0.1768 0.1966 0.1966 27.3312
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 f_dihedral_angle_d 19.4 f_angle_d 0.763 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2458 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 73
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHENIX phasing Coot model building