☰ Navigation Tabs
Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited by ESTERASE B from LACTOBACILLUS RHAMNOSIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N5H PDB entry 4N5H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 1.0 ammonium phosphate, 0.1M TrisHCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.853 α = 90 b = 109.853 β = 90 c = 59.335 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ 2006-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 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 1.44 38.84 89.2 0.081 7.3 3.73 24173 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.49 25.5 0.433 1.4 1.26
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 (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 4N5H 1.96 38.84 25546 24173 1249 99.51 0.16636 0.16421 0.1732 0.20807 0.2146 RANDOM 25.301
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.136 r_dihedral_angle_4_deg 21.221 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_1_deg 6.352 r_angle_refined_deg 1.864 r_angle_other_deg 0.904 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.136 r_dihedral_angle_4_deg 21.221 r_dihedral_angle_3_deg 14.136 r_dihedral_angle_1_deg 6.352 r_angle_refined_deg 1.864 r_angle_other_deg 0.904 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 19
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling