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Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1M Tris pH8.0, 25% PEG 3350, 0.4M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.292 α = 77.43 b = 46.459 β = 75.53 c = 65.981 γ = 69.34
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 300K 2016-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 63.2 94 0.113 0.135 0.073 8 3.3 29472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 83.9 0.313 0.381 0.213 0.864 2.8
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 4BLM 2 43.06 27895 1486 94.27 0.21075 0.20819 0.2136 0.25845 0.2623 RANDOM 16.879
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 31.334 r_dihedral_angle_4_deg 18.882 r_dihedral_angle_3_deg 16.268 r_dihedral_angle_1_deg 7.554 r_long_range_B_refined 4.389 r_long_range_B_other 4.385 r_scangle_other 2.75 r_angle_other_deg 2.393 r_mcangle_it 2.163 r_mcangle_other 2.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.334 r_dihedral_angle_4_deg 18.882 r_dihedral_angle_3_deg 16.268 r_dihedral_angle_1_deg 7.554 r_long_range_B_refined 4.389 r_long_range_B_other 4.385 r_scangle_other 2.75 r_angle_other_deg 2.393 r_mcangle_it 2.163 r_mcangle_other 2.163 r_scbond_it 1.674 r_scbond_other 1.674 r_angle_refined_deg 1.552 r_mcbond_it 1.346 r_mcbond_other 1.346 r_chiral_restr 0.076 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4012 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing