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Crystal structure of the thioesterase domain of the fengycin biosynthesis cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JMK PDB ENTRY 1JMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.2 M NH4 ACETATE; 0.1 M NA CITRATE (PH 5.6); 22.5 % PEG 8000, 10 MG/ML PROTEIN
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.354 α = 90 b = 72.354 β = 90 c = 96.333 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 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2003-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 1.8 24 99.4 0.06 32.7 7.8 26374 -3 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 93.8 0.3 4.1
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 1JMK 1.8 24.35 24923 1337 98.9 0.152 0.15 0.1639 0.188 0.2 RANDOM 17.99
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] 0.7 0.35 0.7 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.84 r_scangle_it 5.197 r_scbond_it 3.15 r_mcangle_it 2.089 r_angle_refined_deg 1.492 r_mcbond_it 1.131 r_angle_other_deg 0.839 r_symmetry_vdw_other 0.307 r_symmetry_hbond_refined 0.279 r_nbd_other 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.84 r_scangle_it 5.197 r_scbond_it 3.15 r_mcangle_it 2.089 r_angle_refined_deg 1.492 r_mcbond_it 1.131 r_angle_other_deg 0.839 r_symmetry_vdw_other 0.307 r_symmetry_hbond_refined 0.279 r_nbd_other 0.249 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.217 r_symmetry_vdw_refined 0.199 r_chiral_restr 0.095 r_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1675 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing