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Crystal Structure of a C8-C4 Sn3 Inhibited Esterase B from Lactobacillus Rhamnosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N5H PDB entry 4N5H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1.0 M ammonium phosphate, 0.1 M TrisHCl, pH 7.2-8.5
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.826 α = 90 b = 109.826 β = 90 c = 59.347 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ Capillary focusing optics and monochromator 2007-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 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 27.1 97 0.116 6.6 4.17 23508 23508 3 21.6
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 2.07 95.9 0.4 2.4 4.14 2269
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 4N5H 2 27.1 22293 22293 1201 97.74 0.16452 0.16452 0.1618 0.1714 0.21512 0.2187 RANDOM 22.402
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] -0.19 -0.19 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.94 r_dihedral_angle_4_deg 21.249 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_1_deg 6.758 r_angle_refined_deg 1.764 r_angle_other_deg 0.928 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.94 r_dihedral_angle_4_deg 21.249 r_dihedral_angle_3_deg 14.523 r_dihedral_angle_1_deg 6.758 r_angle_refined_deg 1.764 r_angle_other_deg 0.928 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2472 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 32
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling