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Pseudomonas fluorescens esterase complexed to the R-enantiomer of a sulfonate transition state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VA4 PDB ENTRY 1VA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.7 M ammonium sulfate, 3% PEG 400, 100 mM sodium-potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.46 72.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.215 α = 90 b = 146.215 β = 90 c = 129.964 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 SI(111) MONOCHROMATOR 2005-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 48.57 97.4 0.056 13.2 3.65 373997 364141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 91.2 0.343 3 2.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1VA4 1.65 48.57 345685 18410 97.35 0.19766 0.19711 0.197 0.20797 0.2082 RANDOM 22.959
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] -1.07 -0.54 -1.07 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 15.867 r_dihedral_angle_3_deg 10.607 r_dihedral_angle_1_deg 4.286 r_scangle_it 1.487 r_scbond_it 0.859 r_angle_refined_deg 0.775 r_mcangle_it 0.565 r_mcbond_it 0.289 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 15.867 r_dihedral_angle_3_deg 10.607 r_dihedral_angle_1_deg 4.286 r_scangle_it 1.487 r_scbond_it 0.859 r_angle_refined_deg 0.775 r_mcangle_it 0.565 r_mcbond_it 0.289 r_chiral_restr 0.061 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12720 Nucleic Acid Atoms Solvent Atoms 1419 Heterogen Atoms 217
Software Software Software Name Purpose CBASS data collection O model building REFMAC refinement d*TREK data reduction d*TREK data scaling