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X-ray crystal structure of pink-colored protein from Pleurotus salmoneostramineus in complex with natural chromophore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other artificial helices without side chain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 PEG4000, sodium formate, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.879 α = 90 b = 31.895 β = 95.939 c = 107.416 γ = 90
Symmetry Space Group I 1 2 1
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 EIGER X 16M 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.25 30.56 99.1 0.071 0.098 0.068 0.99 9.4 3.4 54840
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 1.25 1.27 98.6 0.276 0.383 0.264 0.896 3.8 3.3
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 artificial helices without side chain 1.25 30.56 54839 2826 98.978 0.133 0.1311 0.1302 0.1641 0.1622 14.602
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] 0.684 0.017 -1.524 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.685 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_2_deg 11.799 r_rigid_bond_restr 5.928 r_dihedral_angle_1_deg 4.183 r_lrange_it 3.566 r_lrange_other 3.236 r_scangle_it 3.106 r_scangle_other 3.105 r_scbond_other 2.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.685 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_2_deg 11.799 r_rigid_bond_restr 5.928 r_dihedral_angle_1_deg 4.183 r_lrange_it 3.566 r_lrange_other 3.236 r_scangle_it 3.106 r_scangle_other 3.105 r_scbond_other 2.519 r_scbond_it 2.518 r_angle_refined_deg 1.723 r_mcangle_other 1.587 r_mcangle_it 1.583 r_mcbond_it 1.215 r_mcbond_other 1.208 r_angle_other_deg 0.617 r_nbd_refined 0.259 r_nbd_other 0.222 r_symmetry_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.179 r_symmetry_nbd_refined 0.171 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1657 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing