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The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Morpheus screen condition E12:
37.5% v/v Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350;
0.1M Buffer system 3: 1.0M Tris (base); bicine, pH 8.5
0.12M Additives: 0.3M ethylene glycols
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.676 α = 90 b = 177.34 β = 90 c = 122.416 γ = 90
Symmetry Space Group C 2 2 21
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-F 2018-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.831 90.144 95.7 0.126 0.137 0.053 0.996 9.3 6.6 87249 26.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.831 1.941 58.3 1.278 1.278 0.524 0.599 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YX7 1.831 90.144 87257 4339 87.265 0.161 0.1595 0.1745 0.1983 0.2098 32.791
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] 0.262 -0.452 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.274 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_other_3_deg 13.127 r_lrange_it 6.711 r_lrange_other 6.338 r_dihedral_angle_1_deg 5.18 r_scangle_it 4.005 r_scangle_other 4.005 r_mcangle_other 2.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.274 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_other_3_deg 13.127 r_lrange_it 6.711 r_lrange_other 6.338 r_dihedral_angle_1_deg 5.18 r_scangle_it 4.005 r_scangle_other 4.005 r_mcangle_other 2.558 r_mcangle_it 2.556 r_scbond_it 2.521 r_scbond_other 2.521 r_mcbond_it 1.749 r_mcbond_other 1.745 r_angle_refined_deg 1.547 r_angle_other_deg 1.351 r_nbd_other 0.255 r_symmetry_xyhbond_nbd_refined 0.255 r_symmetry_nbd_refined 0.239 r_xyhbond_nbd_other 0.224 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.135 r_ncsr_local_group_6 0.111 r_ncsr_local_group_5 0.102 r_ncsr_local_group_1 0.099 r_ncsr_local_group_4 0.096 r_ncsr_local_group_2 0.095 r_ncsr_local_group_3 0.092 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7224 Nucleic Acid Atoms Solvent Atoms 928 Heterogen Atoms 936
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling autoPROC data scaling STARANISO data scaling PHASER phasing Coot model building