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Crystal structure of the class C beta-lactamase TRU-1 from Aeromonas enteropelogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% wt/vol PEG-8000, 0.2 M ammonium sulfate and 0.1 M sodium cacodylate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.885 α = 90 b = 78.345 β = 106.63 c = 48.19 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 CCD ADSC QUANTUM 210 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.05 38.35 93.5 0.039 0.043 0.999 18.2 3.6 141631 5.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.11 68 0.114 0.155 0.967 4.7 1.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4GZB 1.05 26.43 134487 7107 93.33 0.11513 0.11438 0.12944 0.1522 RANDOM 8.587
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 32.44 r_sphericity_free 19.427 r_dihedral_angle_4_deg 12.878 r_dihedral_angle_3_deg 12.213 r_sphericity_bonded 8.586 r_dihedral_angle_1_deg 6.713 r_long_range_B_refined 2.47 r_long_range_B_other 2.47 r_rigid_bond_restr 1.575 r_angle_refined_deg 1.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.44 r_sphericity_free 19.427 r_dihedral_angle_4_deg 12.878 r_dihedral_angle_3_deg 12.213 r_sphericity_bonded 8.586 r_dihedral_angle_1_deg 6.713 r_long_range_B_refined 2.47 r_long_range_B_other 2.47 r_rigid_bond_restr 1.575 r_angle_refined_deg 1.476 r_angle_other_deg 0.982 r_mcangle_it 0.954 r_mcangle_other 0.954 r_scangle_other 0.889 r_scbond_it 0.712 r_scbond_other 0.706 r_mcbond_other 0.631 r_mcbond_it 0.63 r_chiral_restr 0.089 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2742 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing