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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 2.05 39.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.154 α = 90 b = 47.154 β = 90 c = 174.226 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 2006-12-18 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 1.81 33.4 88.1 0.054 12 5.24 41855 36866
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 1.81 33.4 21248 20296 1078 99.87 0.197 0.197 0.195 0.2076 0.227 0.2381 RANDOM 29.854
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.83 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_3_deg 10.671 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.311 r_angle_refined_deg 0.996 r_scbond_it 0.934 r_angle_other_deg 0.861 r_mcangle_it 0.632 r_mcbond_it 0.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.83 r_dihedral_angle_4_deg 17.217 r_dihedral_angle_3_deg 10.671 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.311 r_angle_refined_deg 0.996 r_scbond_it 0.934 r_angle_other_deg 0.861 r_mcangle_it 0.632 r_mcbond_it 0.395 r_symmetry_vdw_other 0.291 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.203 r_nbtor_refined 0.176 r_nbd_other 0.173 r_symmetry_hbond_refined 0.104 r_xyhbond_nbd_refined 0.103 r_nbtor_other 0.083 r_mcbond_other 0.067 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1823 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 1
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection Crystal data reduction