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Crystal structure of a fammily VIII carboxylesterase in a complex with cephalothin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 295 2.2 M ammonium sulfate and 0.1 M Tris-HCl (pH 8.5), microbatch, temperature 295KK
Crystal Properties Matthews coefficient Solvent content 5.06 75.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.102 α = 90 b = 149.102 β = 90 c = 172.571 γ = 90
Symmetry Space Group I 4 2 2
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 270 2009-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 0.98000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 89398
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 4IVI 1.8 45.03 84680 4471 99.58 0.16243 0.16139 0.1726 0.18216 0.1934 RANDOM 28.221
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] -1.18 -1.18 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.294 r_sphericity_free 27.141 r_dihedral_angle_4_deg 13.039 r_dihedral_angle_3_deg 12.004 r_sphericity_bonded 8.95 r_dihedral_angle_1_deg 5.566 r_rigid_bond_restr 1.564 r_angle_refined_deg 1.139 r_angle_other_deg 0.749 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.294 r_sphericity_free 27.141 r_dihedral_angle_4_deg 13.039 r_dihedral_angle_3_deg 12.004 r_sphericity_bonded 8.95 r_dihedral_angle_1_deg 5.566 r_rigid_bond_restr 1.564 r_angle_refined_deg 1.139 r_angle_other_deg 0.749 r_chiral_restr 0.069 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3086 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling