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Crystal structure of Phormidium rubidum phycocyanin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YJJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 MPD, PEG1000, PEG3350, Diethylene glycol,
Triethylene glycol, Tetraethylene glycol,
Pentaethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.32 α = 90 b = 106.32 β = 90 c = 58.67 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 2016-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.84920 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.17 39.39 100 1 21.3 14 127070
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.2 0.51
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 4yjj 1.17 39.39 127046 6165 99.973 0.12 0.1188 0.1199 0.145 0.1466 15.305
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] -0.981 -0.491 -0.981 3.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.319 r_dihedral_angle_other_3_deg 33.699 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 4.83 r_rigid_bond_restr 4.404 r_lrange_it 3.81 r_lrange_other 3.15 r_scangle_other 3.127 r_scangle_it 3.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.319 r_dihedral_angle_other_3_deg 33.699 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_3_deg 12.875 r_dihedral_angle_1_deg 4.83 r_rigid_bond_restr 4.404 r_lrange_it 3.81 r_lrange_other 3.15 r_scangle_other 3.127 r_scangle_it 3.126 r_scbond_it 2.454 r_scbond_other 2.453 r_mcangle_it 1.853 r_mcangle_other 1.833 r_angle_refined_deg 1.747 r_angle_other_deg 1.71 r_mcbond_it 1.58 r_mcbond_other 1.56 r_symmetry_nbd_refined 0.307 r_nbd_other 0.279 r_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_other 0.131 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2484 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing