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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 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.848 α = 90 b = 46.848 β = 90 c = 173.954 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 2006-11-21 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 40.57 96.6 0.091 6.5 5.85 30410 29364
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 1.9 40.57 18460 18336 928 99.94 0.208 0.208 0.205 0.2163 0.255 0.2548 RANDOM 42.49
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] 2.67 1.33 2.67 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.582 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_1_deg 6.353 r_scangle_it 2.521 r_scbond_it 1.762 r_angle_refined_deg 1.361 r_mcangle_it 1.168 r_angle_other_deg 0.887 r_mcbond_it 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.582 r_dihedral_angle_3_deg 13.591 r_dihedral_angle_4_deg 12.667 r_dihedral_angle_1_deg 6.353 r_scangle_it 2.521 r_scbond_it 1.762 r_angle_refined_deg 1.361 r_mcangle_it 1.168 r_angle_other_deg 0.887 r_mcbond_it 0.743 r_symmetry_vdw_other 0.297 r_nbd_refined 0.21 r_nbtor_refined 0.186 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_refined 0.153 r_mcbond_other 0.151 r_symmetry_hbond_refined 0.121 r_nbtor_other 0.088 r_chiral_restr 0.078 r_bond_refined_d 0.013 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 1834 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 12
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction