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De novo design of chlorophyll special pair containing protein assemblies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Designed Protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.4 M Sodium malonate dibasic monohydrate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.732 α = 90 b = 88.732 β = 90 c = 149.484 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 3.05 44.37 99.42 0.194 0.999 11.54 10.8 13483 112.91
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 3.05 3.15 96.27 0.248 0.62 10.7
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 Designed Protein 3.05 44.37 1.33 13412 1355 99.46 0.253 0.2482 0.2499 0.2973 0.3012 112.4
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 14.5709 f_angle_d 0.5168 f_chiral_restr 0.0301 f_bond_d 0.0024 f_plane_restr 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3539 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing