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Crystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, phosphate-bound complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1 M sodium acetate pH 4.6, 1.2 M ammonium sulfate, cryoprotectant 8% glycerol, 8% ethylene glycol and 8% sucrose
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.524 α = 90 b = 147.524 β = 90 c = 147.524 γ = 90
Symmetry Space Group P 41 3 2
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 EIGER X 9M 2016-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.27424 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.61 104.32 100 0.181 0.028 1 24.7 77.3 17315
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.68 100 3.313 0.515 0.84 2.6 79.5
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 4KAY 2.61 60.226 1.33 16528 830 95.7 0.2358 0.234 0.2436 0.2705 0.2786 RANDOM
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 13.067 f_angle_d 1.38 f_chiral_restr 0.07 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2602 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing PHENIX model building Coot model building