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Crystal Structure of the Covalent Adduct Formed between TB B-lactamase and Clavulanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GDN PDB entry 2GDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.1 298 0.1 M HEPES pH 7.5, 2 M NH4(H2)PO4, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.666 α = 90 b = 67.655 β = 90 c = 75.032 γ = 90
Symmetry Space Group P 21 21 21
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 2007-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.100 NSLS X12C
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 1.7 41.4 96 0.05 18 3.3 27349 27349 15.76
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 1.74 88 0.4 2 3 1732
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 2GDN 1.7 41.4 25961 1388 95.99 0.18139 0.17974 0.1815 0.21177 0.2121 RANDOM 13.99
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 11.729 r_dihedral_angle_1_deg 11.074 r_scangle_it 3.113 r_scbond_it 2.046 r_angle_refined_deg 1.508 r_mcangle_it 1.094 r_mcbond_it 0.732 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_4_deg 21.684 r_dihedral_angle_3_deg 11.729 r_dihedral_angle_1_deg 11.074 r_scangle_it 3.113 r_scbond_it 2.046 r_angle_refined_deg 1.508 r_mcangle_it 1.094 r_mcbond_it 0.732 r_nbtor_refined 0.302 r_nbd_refined 0.23 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1988 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing