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Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWZ pdb entry 3DWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 4.1 298 0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.657 α = 90 b = 67.922 β = 90 c = 75.546 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 2010-01-21 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 1.3 50 100 0.057 21.4 7.5 63485 63485
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 1.3 1.33 100 0.757 1.8 5.7 4388
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 3DWZ 1.3 26.28 60263 3222 99.96 0.149 0.147 0.1462 0.176 0.1733 RANDOM 13.287
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] 0.03 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 21.341 r_dihedral_angle_3_deg 11.508 r_dihedral_angle_1_deg 6.091 r_scangle_it 4.451 r_scbond_it 3.009 r_mcangle_it 1.959 r_angle_refined_deg 1.428 r_rigid_bond_restr 1.292 r_mcbond_it 1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 21.341 r_dihedral_angle_3_deg 11.508 r_dihedral_angle_1_deg 6.091 r_scangle_it 4.451 r_scbond_it 3.009 r_mcangle_it 1.959 r_angle_refined_deg 1.428 r_rigid_bond_restr 1.292 r_mcbond_it 1.198 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1988 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection DENZO data reduction SCALEPACK data scaling