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Erythromycin esterase EreC, mutant H289N in its closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 295 0.1M phosphate-citrate pH 4.2, 5% (w/v) PEG 3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.21 44.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.366 α = 90 b = 92.678 β = 90 c = 125.795 γ = 90
Symmetry Space Group C 2 2 21
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 Bruker PHOTON II 2018-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 28.152 99.2 0.03177 0.985 35.24 2 27238
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 0.981 8.61
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3B55 2 28.15 1.34 27161 1992 98.1 0.1706 0.1691 0.2149 0.2189
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 11.596 f_angle_d 0.881 f_chiral_restr 0.052 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement PROTEUM PLUS data scaling PDB_EXTRACT data extraction PROTEUM PLUS data reduction PHASER phasing