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Crystal structure of Thermotoga maritima holo-[acyl-carrier-protein] synthase (AcpS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 277 10mM Tris-HCl pH 8.0, 100mM NaCl, 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.35 63.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.96 α = 90 b = 72.96 β = 90 c = 84.22 γ = 120
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 ADSC QUANTUM 315 2014-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.0000 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 63.185 98.2 0.08 0.038 11 5.4 14645 37.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 98.8 0.585 0.272 3.1 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1F80 2.1 63.18 13905 739 98.06 0.17167 0.16915 0.22136 0.2328 RANDOM 52.678
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] -0.09 -0.05 -0.09 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.649 r_sphericity_free 27.582 r_sphericity_bonded 18.603 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_4_deg 9.337 r_dihedral_angle_1_deg 5.061 r_rigid_bond_restr 3.494 r_angle_refined_deg 0.874 r_chiral_restr 0.06 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.649 r_sphericity_free 27.582 r_sphericity_bonded 18.603 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_4_deg 9.337 r_dihedral_angle_1_deg 5.061 r_rigid_bond_restr 3.494 r_angle_refined_deg 0.874 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1354 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing