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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
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 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.322 α = 90 b = 47.322 β = 90 c = 174.741 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 Osmic Blue 2006-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.49 33.52 90.6 0.157 5.1 7.6 38533 34921
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 1R1D 2.2 33.52 11933 11667 578 99.98 0.2 0.2 0.198 0.2083 0.249 0.2515 RANDOM 42.325
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] 1.51 0.75 1.51 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_4_deg 13.851 r_dihedral_angle_1_deg 8.167 r_angle_refined_deg 0.802 r_angle_other_deg 0.682 r_symmetry_vdw_other 0.318 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.225 r_nbd_other 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_4_deg 13.851 r_dihedral_angle_1_deg 8.167 r_angle_refined_deg 0.802 r_angle_other_deg 0.682 r_symmetry_vdw_other 0.318 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.225 r_nbd_other 0.212 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.149 r_nbtor_other 0.104 r_chiral_restr 0.098 r_xyhbond_nbd_other 0.071 r_bond_refined_d 0.023 r_gen_planes_refined 0.021 r_bond_other_d 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1793 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection Crystal data reduction