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Crystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 Morpheus screen condition C9:
10% w/v PEG 20 000, 20% v/v PEG MME 550 precipitants;
0.03 M NPS (Nitrate, Phosphate & Sulfate) mix of additives;
0.01 M bicine/Trizma base pH 8.5 buffer system
Crystal Properties Matthews coefficient Solvent content 2.94 58.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.759 α = 90 b = 192.759 β = 90 c = 524.486 γ = 120
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 2018-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 2.13 159.07 95.6 0.283 0.298 0.093 0.996 8 10.2 156067 29.7
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 2.133 2.322 80.1 1.653 1.749 0.567 0.622 1.6 9.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NB4 2.131 49.005 156062 7765 75.005 0.18 0.1774 0.1875 0.225 0.2312 40.685
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] -0.09 -0.045 -0.09 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.412 r_dihedral_angle_4_deg 18.323 r_dihedral_angle_3_deg 14.236 r_dihedral_angle_other_3_deg 9.212 r_lrange_it 6.056 r_lrange_other 6.013 r_dihedral_angle_1_deg 5.33 r_scangle_other 4.066 r_scangle_it 4.064 r_mcangle_other 3.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.412 r_dihedral_angle_4_deg 18.323 r_dihedral_angle_3_deg 14.236 r_dihedral_angle_other_3_deg 9.212 r_lrange_it 6.056 r_lrange_other 6.013 r_dihedral_angle_1_deg 5.33 r_scangle_other 4.066 r_scangle_it 4.064 r_mcangle_other 3.125 r_mcangle_it 3.123 r_scbond_it 2.639 r_scbond_other 2.639 r_mcbond_it 2.119 r_mcbond_other 2.112 r_angle_refined_deg 1.576 r_angle_other_deg 1.345 r_nbd_refined 0.212 r_nbd_other 0.21 r_symmetry_nbd_other 0.184 r_symmetry_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.161 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.077 r_ncsr_local_group_7 0.062 r_ncsr_local_group_52 0.062 r_ncsr_local_group_20 0.061 r_ncsr_local_group_40 0.061 r_ncsr_local_group_55 0.061 r_ncsr_local_group_31 0.06 r_ncsr_local_group_47 0.059 r_ncsr_local_group_56 0.055 r_chiral_restr_other 0.053 r_ncsr_local_group_25 0.053 r_ncsr_local_group_44 0.053 r_ncsr_local_group_50 0.053 r_ncsr_local_group_54 0.053 r_ncsr_local_group_14 0.05 r_ncsr_local_group_41 0.05 r_ncsr_local_group_49 0.05 r_ncsr_local_group_26 0.049 r_ncsr_local_group_53 0.049 r_ncsr_local_group_22 0.048 r_ncsr_local_group_43 0.048 r_ncsr_local_group_36 0.047 r_ncsr_local_group_42 0.047 r_ncsr_local_group_10 0.045 r_ncsr_local_group_13 0.045 r_ncsr_local_group_21 0.045 r_ncsr_local_group_23 0.045 r_ncsr_local_group_24 0.045 r_ncsr_local_group_48 0.044 r_ncsr_local_group_35 0.041 r_ncsr_local_group_12 0.039 r_ncsr_local_group_51 0.039 r_ncsr_local_group_9 0.038 r_ncsr_local_group_16 0.038 r_ncsr_local_group_32 0.038 r_ncsr_local_group_33 0.038 r_ncsr_local_group_18 0.037 r_ncsr_local_group_5 0.036 r_ncsr_local_group_8 0.036 r_ncsr_local_group_11 0.036 r_ncsr_local_group_39 0.036 r_ncsr_local_group_1 0.035 r_ncsr_local_group_6 0.035 r_ncsr_local_group_17 0.035 r_ncsr_local_group_27 0.035 r_ncsr_local_group_29 0.035 r_ncsr_local_group_30 0.035 r_ncsr_local_group_38 0.035 r_ncsr_local_group_3 0.034 r_ncsr_local_group_15 0.033 r_ncsr_local_group_19 0.033 r_ncsr_local_group_28 0.031 r_ncsr_local_group_34 0.031 r_ncsr_local_group_45 0.031 r_ncsr_local_group_46 0.03 r_ncsr_local_group_2 0.029 r_ncsr_local_group_4 0.029 r_ncsr_local_group_37 0.025 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20592 Nucleic Acid Atoms Solvent Atoms 1365 Heterogen Atoms 4153
Software Software Software Name Purpose REFMAC refinement XDS data processing pointless data scaling Aimless data scaling STARANISO data scaling PHASER phasing XDS data reduction