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High resolution 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 G8
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.046 α = 78.76 b = 110.17 β = 82.28 c = 118.516 γ = 60.43
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 2017-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.38 95.42 95.7 0.077 0.077 0.997 7.3 2.9 932250 8.2
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 1.38 1.42 93.2 0.801 0.801 0.477 1.3 2.8
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 1.38 95.42 878170 46444 94.7 0.158 0.155 0.1562 0.211 0.2118 RANDOM 15.91
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] -0.15 0.08 0.27 -0.18 -0.36 0.41
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.746 r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_3_deg 12.717 r_sphericity_bonded 10.923 r_long_range_B_refined 5.757 r_dihedral_angle_1_deg 5.119 r_long_range_B_other 3.615 r_rigid_bond_restr 3.107 r_scangle_other 2.655
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.746 r_dihedral_angle_2_deg 35.364 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_3_deg 12.717 r_sphericity_bonded 10.923 r_long_range_B_refined 5.757 r_dihedral_angle_1_deg 5.119 r_long_range_B_other 3.615 r_rigid_bond_restr 3.107 r_scangle_other 2.655 r_angle_refined_deg 2.596 r_scbond_it 2.221 r_scbond_other 2.216 r_mcangle_it 1.977 r_mcangle_other 1.977 r_mcbond_it 1.621 r_mcbond_other 1.621 r_angle_other_deg 1.284 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_other 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.003 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 7799 Heterogen Atoms 2762
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing