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Atomic resolution structure of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294.15 Morpheus screen condition C8 with the NPS mix of additives
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.046 α = 78.78 b = 109.095 β = 82.32 c = 117.371 γ = 60.26
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 2016-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.14 94.62 93.8 0.042 0.042 0.998 10.7 2.6 1575226 9.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.16 90 0.545 0.545 0.601 1.6 2.7
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 FOURIER SYNTHESIS THROUGHOUT 5aqd 1.14 94.62 1496003 79188 93.8 0.149 0.147 0.1486 0.184 0.1851 RANDOM 15.58
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] -0.07 0.11 -0.47 -0.5 0.09 0.95
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.964 r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 17.023 r_dihedral_angle_3_deg 12.897 r_sphericity_bonded 12.278 r_long_range_B_refined 5.975 r_dihedral_angle_1_deg 5.071 r_long_range_B_other 4.31 r_mcangle_it 3.105 r_mcangle_other 3.105
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.964 r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 17.023 r_dihedral_angle_3_deg 12.897 r_sphericity_bonded 12.278 r_long_range_B_refined 5.975 r_dihedral_angle_1_deg 5.071 r_long_range_B_other 4.31 r_mcangle_it 3.105 r_mcangle_other 3.105 r_angle_refined_deg 2.682 r_scangle_other 2.589 r_mcbond_it 2.45 r_mcbond_other 2.45 r_scbond_it 2.229 r_scbond_other 2.219 r_rigid_bond_restr 2.203 r_angle_other_deg 1.216 r_chiral_restr 0.114 r_gen_planes_other 0.018 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31032 Nucleic Acid Atoms Solvent Atoms 8168 Heterogen Atoms 2836
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data collection Aimless data scaling Coot model building REFMAC phasing