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Crystal structure of class C beta-lactamase PDC-16 in complex with imipenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350,100mM HEPES pH-7.5,225mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.16 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.82 α = 90 b = 90.02 β = 90 c = 103.11 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 IMAGE PLATE MARRESEARCH MIRROR 2025-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 2.2 51.61 99.91 0.998 5.94 9.6 35116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.099 0.11
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6S1S 2.2 51.608 35066 1788 99.909 0.189 0.186 0.1888 0.2451 0.2485 RANDOM 32.825
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] -2.413 4.697 -2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.662 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_2_deg 12.53 r_lrange_it 8.074 r_lrange_other 8.032 r_dihedral_angle_1_deg 7.32 r_scangle_it 5.679 r_scangle_other 5.678 r_mcangle_it 4.749 r_mcangle_other 4.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.662 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_2_deg 12.53 r_lrange_it 8.074 r_lrange_other 8.032 r_dihedral_angle_1_deg 7.32 r_scangle_it 5.679 r_scangle_other 5.678 r_mcangle_it 4.749 r_mcangle_other 4.749 r_scbond_it 3.651 r_scbond_other 3.65 r_mcbond_it 3.171 r_mcbond_other 3.171 r_angle_refined_deg 1.702 r_angle_other_deg 0.575 r_symmetry_xyhbond_nbd_refined 0.297 r_nbd_other 0.258 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.186 r_symmetry_nbd_refined 0.152 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5564 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction pointless data scaling PHASER phasing