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Apo structure of Class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IYO PDB ENTRY 1IYO
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 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.545 α = 90 b = 72.545 β = 90 c = 97.656 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 2007-12-10 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 0.94 50 99.9 0.075 25.99 10.1 192768
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) 0.94 0.96 98.9 0.384 4.32 5.7
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 1IYO 0.94 50 182648 9670 99.92 0.1358 0.13519 0.1362 0.14726 0.1481 RANDOM 10.475
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] -0.23 -0.12 -0.23 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_4_deg 13.007 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 6.354 r_sphericity_free 5.02 r_sphericity_bonded 4.634 r_scangle_it 3.159 r_scbond_it 2.314 r_mcangle_it 1.847 r_angle_refined_deg 1.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_4_deg 13.007 r_dihedral_angle_3_deg 10.695 r_dihedral_angle_1_deg 6.354 r_sphericity_free 5.02 r_sphericity_bonded 4.634 r_scangle_it 3.159 r_scbond_it 2.314 r_mcangle_it 1.847 r_angle_refined_deg 1.495 r_mcbond_it 1.285 r_rigid_bond_restr 1.049 r_nbtor_refined 0.307 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2267 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 30
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling