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Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E04 4E04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% PEG1000
10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.806 α = 90 b = 98.708 β = 90 c = 156.833 γ = 90
Symmetry Space Group I 2 2 2
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 2019-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.015 69.7 75.4 0.03 0.9994 14.257 13.6 30361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.015 2.182 1.406 0.2832
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 4E04 2.015 19.99 30312 1533 75.4 0.2422 0.2401 0.2319 0.28 0.2841 RANDOM 57.27
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] -1.2082 1.2931 -0.0849
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.21 t_omega_torsion 3.17 t_angle_deg 1.11 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.21 t_omega_torsion 3.17 t_angle_deg 1.11 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4247 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling MOLREP phasing