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X-ray structure of phycoerythrin from Porphyridium cruentum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PE crystals were grown by hanging drop vapor diffusion method (Russo Krauss et al., 2013) using a drop containing 10 mg/mL PE in 0.250 M ammonium sulphate, 25.0 mM potassium phosphate at pH 5.0, equilibrated with a reservoir containing 0.500 M ammonium sulphate, 50.0 mM potassium phosphate at pH 5.0.
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.59 α = 90 b = 186.59 β = 90 c = 59.19 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 2022-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 1.597 46.648 99 0.101 0.107 0.035 0.997 12.9 9.2 100909
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 1.597 1.625 98.3 1.028 0.999 0.36 0.595 2.2 9
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 3V58 1.6 46.648 100412 4971 98.994 0.223 0.2217 0.2259 0.2564 0.2599 23.932
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] -0.061 -0.031 -0.061 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 5.821 r_lrange_it 4.18 r_lrange_other 4.143 r_scangle_it 3.373 r_scangle_other 3.368 r_mcangle_it 2.439 r_mcangle_other 2.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 5.821 r_lrange_it 4.18 r_lrange_other 4.143 r_scangle_it 3.373 r_scangle_other 3.368 r_mcangle_it 2.439 r_mcangle_other 2.439 r_scbond_it 2.387 r_scbond_other 2.377 r_mcbond_it 1.862 r_mcbond_other 1.861 r_angle_refined_deg 1.602 r_angle_other_deg 1.477 r_nbd_refined 0.284 r_xyhbond_nbd_other 0.238 r_symmetry_nbd_other 0.209 r_xyhbond_nbd_refined 0.18 r_nbd_other 0.174 r_nbtor_refined 0.166 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.161 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5070 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 458
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing