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Ceftazidime acyl-intermediate structure of class a beta-lact 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 2.61 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.413 α = 90 b = 72.413 β = 90 c = 97.665 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 CCD RIGAKU JUPITER 210 mirrors 2008-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.7 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 1.19 50 100 0.056 42.97 10.4 95363
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) 1.19 1.21 99.8 0.375 5.02 7.8
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 1.19 50 90431 4777 99.97 0.13972 0.13869 0.1369 0.1587 0.1577 RANDOM 12.746
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] -0.08 -0.04 -0.08 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.78 r_dihedral_angle_3_deg 10.615 r_dihedral_angle_4_deg 10.128 r_dihedral_angle_1_deg 6.301 r_sphericity_free 6.002 r_sphericity_bonded 4.39 r_scangle_it 3.6 r_scbond_it 2.823 r_rigid_bond_restr 1.943 r_mcangle_it 1.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.78 r_dihedral_angle_3_deg 10.615 r_dihedral_angle_4_deg 10.128 r_dihedral_angle_1_deg 6.301 r_sphericity_free 6.002 r_sphericity_bonded 4.39 r_scangle_it 3.6 r_scbond_it 2.823 r_rigid_bond_restr 1.943 r_mcangle_it 1.827 r_angle_refined_deg 1.494 r_mcbond_it 1.26 r_nbtor_refined 0.308 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 2181 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 51
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling