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Crystal structure of class A beta-lactamase of Bacillus licheniformis BS3 with aminocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W7F PDB ENTRY 1W7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7.2 293 5micro-l of a protein solution (at a concentration of 38mg/ml in 50mM NaCl, 10mM Tris buffer, pH 7.2), 4micro-l of 8% PEG 6000 in 100mM sodium aminocitrate buffer (pH 3.4) plus 1micro-l of 0.1M urea additive, equilibrated against 1ml of a 20% PEG 6000, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.665 α = 90 b = 104.71 β = 93.96 c = 63.884 γ = 90
Symmetry Space Group P 1 21 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 MAR scanner 345 mm plate mirrors 2005-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.5 63.758 82.3 0.083 0.083 7.6 1.9 17440
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) 2.5 2.64 75.5 0.371 0.371 1.9 1.7 2310
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 1W7F 2.5 36.47 17393 887 81.88 0.223 0.22 0.2161 0.288 0.2836 RANDOM 22.959
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] 0.05 0.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.223 r_dihedral_angle_3_deg 19.146 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_1_deg 7.666 r_scangle_it 2.964 r_scbond_it 1.857 r_angle_refined_deg 1.834 r_mcangle_it 1.354 r_mcbond_it 0.778 r_symmetry_hbond_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.223 r_dihedral_angle_3_deg 19.146 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_1_deg 7.666 r_scangle_it 2.964 r_scbond_it 1.857 r_angle_refined_deg 1.834 r_mcangle_it 1.354 r_mcbond_it 0.778 r_symmetry_hbond_refined 0.316 r_nbtor_refined 0.315 r_nbd_refined 0.286 r_symmetry_vdw_refined 0.268 r_xyhbond_nbd_refined 0.226 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3988 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 26
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction