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Crystal structure of chorismate mutase like domain of bifunctional DAHP synthase of Bacillus subtilis in complex with Chlorogenic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.685 α = 90 b = 47.049 β = 107.23 c = 56.797 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 345 mm plate 2015-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54
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 50 98 0.06 24.58 3.4 16372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 88 0.266 0.926 3.76 2.7
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 3NVT 1.8 50 15497 875 97.84 0.17728 0.17514 0.1843 0.21523 0.2326 RANDOM 32.143
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] -0.74 -1.81 0.23 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 24.86 r_dihedral_angle_3_deg 13.431 r_long_range_B_other 7.774 r_long_range_B_refined 7.695 r_dihedral_angle_1_deg 5.844 r_scangle_other 5.007 r_scbond_it 3.423 r_scbond_other 3.322 r_mcangle_it 3.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 24.86 r_dihedral_angle_3_deg 13.431 r_long_range_B_other 7.774 r_long_range_B_refined 7.695 r_dihedral_angle_1_deg 5.844 r_scangle_other 5.007 r_scbond_it 3.423 r_scbond_other 3.322 r_mcangle_it 3.059 r_mcangle_other 3.058 r_mcbond_it 2.195 r_mcbond_other 2.128 r_angle_refined_deg 1.769 r_angle_other_deg 0.942 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1391 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing SCALA data reduction MOLREP phasing