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Crystal structure of the two-domain non-ribosomal peptide synthetase EntB containing isochorismate lyase and aryl-carrier protein domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NF9 pdb entry 1NF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 10-15% mePEG5000,
0.8M MgCl2,
10% ethylene glycol,
50mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.889 α = 90 b = 82.331 β = 90 c = 164.73 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV Osmic Max-Flux Confocal Mirrors 2004-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.3 25 96.3 0.063 15.5 3.8 31192 30038 47.8
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 2.3 2.38 80 0.341 2423
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1NF9 2.3 25 31509 29972 1545 95.12 0.189 0.189 0.186 0.1862 0.241 0.2389 RANDOM 45.001
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] 3.1 0.15 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.562 r_scangle_it 5.162 r_mcangle_it 4.44 r_scbond_it 3.995 r_mcbond_it 3.28 r_angle_refined_deg 1.245 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.024 r_dihedral_angle_4_deg 18.551 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.562 r_scangle_it 5.162 r_mcangle_it 4.44 r_scbond_it 3.995 r_mcbond_it 3.28 r_angle_refined_deg 1.245 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4418 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 14
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction PHASER phasing