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Crystal structure of Phycoerythrin from Halomicronema Sp. R31DM
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 298 0.2 M Potassium sodium
tartrate, 20% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.59 α = 78.37 b = 108.63 β = 82.53 c = 116.93 γ = 62.11
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MARRESEARCH 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.979 RRCAT INDUS-2 PX-BL21
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 2.21 42.17 97.3 0.997 15.6 3.9 225119
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 2.21 2.21 0.974
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 MOLECULAR REPLACEMENT THROUGHOUT 5NB4 2.21 42.17 214013 11103 97.23 0.1654 0.1631 0.1725 0.2101 0.2169 RANDOM 17.951
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] -0.31 -0.12 -0.16 -0.65 -0.16 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.966 r_dihedral_angle_4_deg 15.788 r_dihedral_angle_3_deg 14.388 r_dihedral_angle_1_deg 5.961 r_angle_refined_deg 1.575 r_angle_other_deg 1.375 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.966 r_dihedral_angle_4_deg 15.788 r_dihedral_angle_3_deg 14.388 r_dihedral_angle_1_deg 5.961 r_angle_refined_deg 1.575 r_angle_other_deg 1.375 r_chiral_restr 0.083 r_bond_refined_d 0.009 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 31086 Nucleic Acid Atoms Solvent Atoms 2776 Heterogen Atoms 2580
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling PHASER phasing