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Cefotaxime acyl-intermediate structure of class a beta-lacta Toho-1 E166A/R274N/R276N triple mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZQ7 PDB ENTRY 2ZQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.95-2.10M ammonium sulfate, 0.2M sodium citrate, PH5.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.522 α = 90 b = 72.522 β = 90 c = 97.96 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 100 IMAGE PLATE RIGAKU RAXIS V mirrors 2007-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.8 SPring-8 BL26B1
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 0.95 50 99.7 0.076 25.88 10.3 186625
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 0.95 0.97 95.7 0.392 4.77 6.7
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 2ZQ7 0.95 50 177014 9369 99.67 0.13557 0.13507 0.1354 0.14487 0.1449 RANDOM 10.501
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] -0.14 -0.07 -0.14 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.066 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_3_deg 10.361 r_dihedral_angle_1_deg 6.469 r_sphericity_free 4.684 r_sphericity_bonded 4.155 r_scangle_it 3.072 r_scbond_it 2.153 r_mcangle_it 1.7 r_angle_refined_deg 1.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.066 r_dihedral_angle_4_deg 12.815 r_dihedral_angle_3_deg 10.361 r_dihedral_angle_1_deg 6.469 r_sphericity_free 4.684 r_sphericity_bonded 4.155 r_scangle_it 3.072 r_scbond_it 2.153 r_mcangle_it 1.7 r_angle_refined_deg 1.539 r_mcbond_it 1.171 r_rigid_bond_restr 0.994 r_nbtor_refined 0.306 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1966 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 46
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling