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X-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an Escherichia coli with a Tripeptide Deletion (Gly286 Ser287 Asp288) on the H10 Helix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BLS PDB ENTRY 2BLS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 10mM Hepes, 20% PEG 4000, 5% iso-propanol, 0.05M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.065 α = 82.62 b = 47.381 β = 80.91 c = 81.461 γ = 65.4
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 315 2006-11-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.07158 SPring-8 BL41XU 2 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
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 1,2 1.7 50 0.062 18.1 2.2 65343
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) 1.7 1.76 0.267 2.6
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 2BLS 1.7 39.16 62030 3287 94.1 0.16527 0.16314 0.1628 0.20557 0.2048 RANDOM 16.863
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.577 r_dihedral_angle_4_deg 15.733 r_dihedral_angle_3_deg 14.565 r_dihedral_angle_1_deg 5.607 r_scangle_it 3.849 r_scbond_it 2.378 r_angle_refined_deg 1.4 r_mcangle_it 1.372 r_mcbond_it 0.76 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.577 r_dihedral_angle_4_deg 15.733 r_dihedral_angle_3_deg 14.565 r_dihedral_angle_1_deg 5.607 r_scangle_it 3.849 r_scbond_it 2.378 r_angle_refined_deg 1.4 r_mcangle_it 1.372 r_mcbond_it 0.76 r_nbtor_refined 0.312 r_nbd_refined 0.217 r_metal_ion_refined 0.215 r_symmetry_vdw_refined 0.166 r_symmetry_metal_ion_refined 0.135 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.102 r_bond_refined_d 0.012 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 5796 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing