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Structural and mechanistic studies on a cephalosporin esterase from the clavulanic acid biosynthesis pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XEP PDB ENTRY 2XEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 13%(W/V) PEG4000,0.1M NAAC,0.1M NACL,10%(W/V) GLYCEROL,0.1M TRIS/HCL PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.514 α = 90 b = 100.895 β = 93.94 c = 81.355 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2008-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 1.8 81.1 98.1 0.1 3.7 89909
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 1.8 1.86 91.3 0.25 3.1
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 2XEP 1.8 81.11 85397 4497 98.09 0.19862 0.19706 0.1955 0.22821 0.2259 RANDOM 22.061
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] -0.75 -0.5 0.7 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.895 r_dihedral_angle_4_deg 15.887 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 5.476 r_scangle_it 3.5 r_scbond_it 2.226 r_angle_refined_deg 1.768 r_mcangle_it 1.341 r_mcbond_it 0.853 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.895 r_dihedral_angle_4_deg 15.887 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 5.476 r_scangle_it 3.5 r_scbond_it 2.226 r_angle_refined_deg 1.768 r_mcangle_it 1.341 r_mcbond_it 0.853 r_nbtor_refined 0.302 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.145 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 6538 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing