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X-ray crystal structure of the extended-spectrum AmpC Y221G mutant beta-lactamase at 1.90 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KE4 PDB entry 1KE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293 1.7M KPi, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.717 α = 90 b = 76.789 β = 116.62 c = 98.693 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 4 mirrors 2008-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 88.388 99.9 0.071 0.071 18.1 5.1 61926 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 100 0.277 0.277 2.1 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Rigid body refinement from wild-type structure THROUGHOUT PDB entry 1KE4 1.9 30 61974 58776 3134 99.93 0.15919 0.15718 0.1581 0.19671 0.1986 RANDOM 18.663
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] 0.67 0.73 -0.19 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.574 r_dihedral_angle_4_deg 17.171 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 6.155 r_scangle_it 3.878 r_scbond_it 2.36 r_mcangle_it 1.463 r_angle_refined_deg 1.443 r_mcbond_it 0.798 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.574 r_dihedral_angle_4_deg 17.171 r_dihedral_angle_3_deg 13.277 r_dihedral_angle_1_deg 6.155 r_scangle_it 3.878 r_scbond_it 2.36 r_mcangle_it 1.463 r_angle_refined_deg 1.443 r_mcbond_it 0.798 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5552 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 74
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction