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Structure of beta-lactamase TEM-171
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG-4000, 0.2 M calcium acetate, 0.1 M Tris-HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.19 α = 90 b = 88.19 β = 90 c = 499.323 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976300 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.999 86.85 98.6 0.99 18.5 13.2 132474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.999 2.05 0.787
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3JYI 1.999 15 132051 6526 97.834 0.191 0.1899 0.2011 0.2106 0.2097 58.018
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] 1.363 1.363 -2.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.463 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.932 r_lrange_it 7.314 r_lrange_other 7.257 r_dihedral_angle_1_deg 6.406 r_scangle_it 2.418 r_scangle_other 2.418 r_mcangle_it 1.901 r_mcangle_other 1.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.463 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.932 r_lrange_it 7.314 r_lrange_other 7.257 r_dihedral_angle_1_deg 6.406 r_scangle_it 2.418 r_scangle_other 2.418 r_mcangle_it 1.901 r_mcangle_other 1.901 r_angle_refined_deg 1.558 r_scbond_it 1.448 r_scbond_other 1.448 r_angle_other_deg 1.356 r_mcbond_it 1.17 r_mcbond_other 1.17 r_nbd_other 0.229 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.195 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.153 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12168 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing