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Structure of a far-red fluorescent biliprotein derived from a far-red induced allophycocyanin F subunit from a thermophilic cyanobacterium Chroococcidiopsis thermalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (v/v) 2-propanol
0.1 M MES monohydrate pH 6.0
20% (w/v) PEGMME 2000
Crystal Properties Matthews coefficient Solvent content 2.13 42.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.248 α = 90 b = 74.823 β = 90.67 c = 61.031 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 4M 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.52 50 93 0.2956 4.28 5.3 17506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.61 90 0.8865 1.24 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CPC 2.52 47.39 16526 870 92.46 0.27695 0.27412 0.2397 0.33173 0.2919 RANDOM 35.624
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] -1.75 -24.98 -14 15.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.095 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 4.806 r_angle_other_deg 3.279 r_long_range_B_refined 2.064 r_long_range_B_other 2.064 r_angle_refined_deg 1.479 r_mcangle_it 1.178 r_mcangle_other 1.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.095 r_dihedral_angle_3_deg 15.512 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 4.806 r_angle_other_deg 3.279 r_long_range_B_refined 2.064 r_long_range_B_other 2.064 r_angle_refined_deg 1.479 r_mcangle_it 1.178 r_mcangle_other 1.178 r_scangle_other 0.804 r_mcbond_it 0.655 r_mcbond_other 0.655 r_scbond_it 0.458 r_scbond_other 0.458 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4079 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement xia2 data reduction autoPROC data scaling PHASER phasing