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Light harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in an alternating tight to loose interface filament
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LMX 4LMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 25% PEG3350 (w/v) + 2% (w/v) Benzamidine HCl, 150 nL mother + 150 nl protein solution, Cryoprotectant of 20% Gylcerol
Crystal Properties Matthews coefficient Solvent content 1.78 30.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.856 α = 90 b = 75.596 β = 110.304 c = 99.36 γ = 90
Symmetry Space Group P 1 21 1
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 16M 2020-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.67 61.7 100 0.091 0.999 9.5 6.7 104433 28
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 1.67 1.7 0.406 0.7
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 FREE R-VALUE 4LMX 1.67 61.66 1.33 104107 1998 99.69 0.1866 0.1858 0.1862 0.2314 0.2295 39.11
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 17.1047 f_angle_d 1.4464 f_chiral_restr 0.0633 f_bond_d 0.0131 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8713 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 896
Software Software Software Name Purpose PHENIX refinement Coot model building DIALS data reduction Aimless data scaling PHENIX phasing