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Light harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in a tight 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 PEG3350 25% (w/v) + 0.01M Sarcosine, 150 nL mother + 150 nL protein solution, Cryoprotectant of 20% Gylcerol
Crystal Properties Matthews coefficient Solvent content 1.62 23.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.529 α = 90 b = 71.258 β = 108.466 c = 48.283 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 1.73 45.8 100 0.135 0.997 8.2 6.5 42700 27.02
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 1.73 1.76 0.355 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 1.73 45.8 1.34 42408 1972 99.34 0.1902 0.1877 0.1894 0.2392 0.2398 35.85
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 17.744 f_angle_d 1.4149 f_chiral_restr 0.0614 f_bond_d 0.0131 f_plane_restr 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4210 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 430
Software Software Software Name Purpose Coot model building PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing