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Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R1D PDB ENTRY 1R1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 6 298 PEG 8000, Na acetate, pH 6.0, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.225 α = 90 b = 47.225 β = 90 c = 174.572 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV CONFOCAL 2006-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.6 30 99.8 0.048 25.4 10.9 30909 30848
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 1R1D 1.6 29.84 30917 30844 1549 99.8 0.167 0.167 0.167 0.1692 0.184 0.1862 RANDOM 20.895
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_4_deg 10.755 r_dihedral_angle_1_deg 5.865 r_scangle_it 2.335 r_scbond_it 1.636 r_angle_refined_deg 1.234 r_mcangle_it 1.004 r_angle_other_deg 0.89 r_mcbond_it 0.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_4_deg 10.755 r_dihedral_angle_1_deg 5.865 r_scangle_it 2.335 r_scbond_it 1.636 r_angle_refined_deg 1.234 r_mcangle_it 1.004 r_angle_other_deg 0.89 r_mcbond_it 0.622 r_symmetry_vdw_other 0.297 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.22 r_nbtor_refined 0.183 r_nbd_other 0.179 r_mcbond_other 0.158 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.107 r_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 8
Software Software Software Name Purpose d*TREK data scaling SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction