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Crystal structure of an adenylation domain interrupted by a methylation domain (AMA4) from nonribosomal peptide synthetase TioS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GR5 PDB entry 4GR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.12 M calcium chloride, 0.1 M HEPES, pH 7.0, 22% PEG400
Crystal Properties Matthews coefficient Solvent content 5.5 77.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.712 α = 90 b = 136.712 β = 90 c = 228.234 γ = 120
Symmetry Space Group P 32 2 1
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 RAYONIX MX300-HS 2016-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 50 99.4 0.097 18 3.5 54895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.9 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4GR5 2.9 40 52034 2855 99.3 0.23657 0.23566 0.2351 0.25316 0.2514 RANDOM 85.178
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] 2.75 1.38 2.75 -8.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.253 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_4_deg 12.749 r_long_range_B_refined 6.048 r_long_range_B_other 6.048 r_dihedral_angle_1_deg 5.267 r_mcangle_it 5.001 r_mcangle_other 5 r_mcbond_it 3.001 r_mcbond_other 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.253 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_4_deg 12.749 r_long_range_B_refined 6.048 r_long_range_B_other 6.048 r_dihedral_angle_1_deg 5.267 r_mcangle_it 5.001 r_mcangle_other 5 r_mcbond_it 3.001 r_mcbond_other 3.001 r_scangle_other 2.798 r_scbond_it 1.526 r_scbond_other 1.526 r_angle_refined_deg 1.146 r_angle_other_deg 0.908 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.005 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 7277 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing