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Crystal structure of beta-lactamase PenP mutant-E166H in complex with cephaloridine as "post-acylation" intermediate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1M Tris pH 8.0, 22.5% PEG 3350, 0.4M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.96 37.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.24 α = 76.84 b = 45.94 β = 75.58 c = 65.99 γ = 69.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ 2013-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.005 63.155 93.3 0.068 0.079 0.04 14.2 3.9 28415 28415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.11 89.1 0.239 0.239 0.276 0.139 3.2 3.9 3964
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.1 38 23641 1263 93.95 0.1982 0.1958 0.2025 0.2404 0.2432 RANDOM 21.174
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] 0.09 -0.03 0.08 -0.03 -0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_3_deg 15.113 r_dihedral_angle_1_deg 7.237 r_angle_refined_deg 1.173 r_angle_other_deg 0.676 r_chiral_restr 0.074 r_gen_planes_refined 0.011 r_bond_refined_d 0.007 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_3_deg 15.113 r_dihedral_angle_1_deg 7.237 r_angle_refined_deg 1.173 r_angle_other_deg 0.676 r_chiral_restr 0.074 r_gen_planes_refined 0.011 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4008 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data collection PDB_EXTRACT data extraction SCALA data reduction SCALA data scaling PHASER phasing