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Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" 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 33500, 4M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.24 α = 77.63 b = 45.88 β = 75.51 c = 66.09 γ = 69.27
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 RIGAKU RAXIS IV++ 2013-11-14 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) 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 1.93 42.49 92.8 0.051 0.059 0.03 0.998 18.3 3.9 32004
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 1.93 2.03 87.7 0.134 0.156 0.079 0.981 8.4 3.9
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 1.93 35.1 30373 1624 92.78 0.17952 0.17751 0.1854 0.21759 0.2256 RANDOM 13.767
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 32.84 r_dihedral_angle_4_deg 17.394 r_dihedral_angle_3_deg 15.026 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 4.632 r_long_range_B_other 4.63 r_scangle_other 3.101 r_angle_other_deg 2.352 r_scbond_it 1.896 r_scbond_other 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 17.394 r_dihedral_angle_3_deg 15.026 r_dihedral_angle_1_deg 6.984 r_long_range_B_refined 4.632 r_long_range_B_other 4.63 r_scangle_other 3.101 r_angle_other_deg 2.352 r_scbond_it 1.896 r_scbond_other 1.896 r_mcangle_it 1.854 r_mcangle_other 1.854 r_angle_refined_deg 1.834 r_mcbond_it 1.162 r_mcbond_other 1.153 r_chiral_restr 0.089 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.01 r_gen_planes_refined 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 4036 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing