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1.8 Angstrom crystal structure of IMP-1 metallo-beta-lactamase with a mixed iron-zinc center in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DOO PDB ENTRY 2DOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 drop contained 1ul protein (25-30mg/ml in 20mm HEPES, 50mm NaCl, ph7.5) with 1uL microseed reservoir (0.2M sodium acetate, 0.2M sodium citrate, 26% PEGMME 2K). Protein solution was heat-treated at 310K for 3-5 days prior to filtration and crystallisation screening. microseeding was essential for diffraction quality crystal growth. crystal grew over 2 weeks
Crystal Properties Matthews coefficient Solvent content 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.99 α = 83.45 b = 75.91 β = 75.3 c = 82.36 γ = 74.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 210r 2013-03-14 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 210r 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1.283500 Australian Synchrotron MX1 2 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 1.7311 Australian Synchrotron MX1
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 1.8 44.93 94.81 0.05521 18.08 3.9 381468 19.81
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 1.8 1.85 92.26 0.4806 0.569 2.9 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 2DOO 1.8 44.927 1.99 191266 9681 91.74 0.1625 0.1615 0.1641 0.182 0.1837 Random Selection 34.3635
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 f_dihedral_angle_d 11.528 f_angle_d 0.962 f_chiral_restr 0.037 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6900 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 80
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement Coot model building PHASER phasing XSCALE data scaling XDS data reduction Blu-Ice data collection