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Crystal structure of Truncated (Delta 1-19) Chitoporin VhChiP from Vibrio harveyi in complex with chitohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.8 292 10 mM GlcNAc6 , 0.125 M Lithium nitrate, 0.1 M Glycine pH 9.8, 45 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 4.33 71.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58 α = 65.799 b = 131.226 β = 87.826 c = 136.586 γ = 86.897
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors 2020-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.9 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.7 20 100 0.169 0.138 0.188 0.081 0.75 37.7 5.1 98809 45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.03 0.996
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 5MDO 2.75003171354 19.8910427457 1.96346217736 85897 4784 90.3627259147 0.182204428945 0.179783098027 0.1816 0.222748080602 0.2243 43.2929439915
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 15.291946525 f_angle_d 1.04170570672 f_chiral_restr 0.0539399728953 f_bond_d 0.00908216321593 f_plane_restr 0.005091397952
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15462 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 684
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing