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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 3DKR
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 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.442 α = 90 b = 47.442 β = 90 c = 174.18 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 2006-12-08 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 1.6 33.54 94.4 0.048 14.5 4.4 31093 29366
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 3DKR 1.72 33.54 25016 24097 1241 95.84 0.178 0.178 0.177 0.1871 0.201 0.2102 RANDOM 25.404
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] 0.33 0.16 0.33 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 11.56 r_dihedral_angle_1_deg 5.199 r_scangle_it 1.741 r_scbond_it 1.131 r_angle_refined_deg 1.03 r_mcangle_it 0.688 r_mcbond_it 0.405 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 11.56 r_dihedral_angle_1_deg 5.199 r_scangle_it 1.741 r_scbond_it 1.131 r_angle_refined_deg 1.03 r_mcangle_it 0.688 r_mcbond_it 0.405 r_nbtor_refined 0.304 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.091 r_xyhbond_nbd_refined 0.085 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction