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Crystal structure of the substrate binding protein from Microbacterium hydrocarbonoxydans complexed with propylparaben
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium acetate
0.1 M sodium cacodylate, pH 7.5
30% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.083 α = 90 b = 77.17 β = 90 c = 121.35 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 95 PIXEL DECTRIS PILATUS3 S 6M 2018-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.8 50 98.8 0.152 0.974 35.4 3.2 12261
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 2.8 2.85 98.8 0.413 0.794 2.2 3.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6LU3 2.8 47.743 12231 618 98.852 0.209 0.2072 0.2078 0.247 0.2474 44.864
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] -2.179 2.129 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 19.653 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_1_deg 10.668 r_lrange_it 4.87 r_lrange_other 4.87 r_scangle_it 3.171 r_scangle_other 3.17 r_mcangle_it 3.099 r_mcangle_other 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 19.653 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_1_deg 10.668 r_lrange_it 4.87 r_lrange_other 4.87 r_scangle_it 3.171 r_scangle_other 3.17 r_mcangle_it 3.099 r_mcangle_other 3.099 r_angle_other_deg 2.424 r_mcbond_it 1.934 r_mcbond_other 1.934 r_scbond_it 1.887 r_scbond_other 1.886 r_angle_refined_deg 1.359 r_symmetry_nbd_other 0.219 r_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.197 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.16 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.055 r_bond_other_d 0.037 r_gen_planes_other 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3544 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing