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Phytochromobilin-adducted PAS-GAF bidomain of Sorghum bicolor phyB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 283.15 100 mM Tris/HCl pH 8.5, 500 mM NaCl, 9% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.875 α = 90 b = 133.875 β = 90 c = 46.951 γ = 120
Symmetry Space Group P 31 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 PILATUS3 6M 2017-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.1 43.82 99.1 0.151 0.175 0.088 0.997 10.7 7.4 28169 38.875
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 2.1 2.16 98.5 1.62 1.873 0.933 0.536 1.3 7.7
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 6TBY 2.1 43.82 28161 1401 98.974 0.199 0.197 0.2055 0.2295 0.2361 38.875
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] -0.003 -0.001 -0.003 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.166 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_other_3_deg 13.943 r_lrange_it 8.538 r_lrange_other 8.492 r_dihedral_angle_1_deg 7.532 r_scangle_it 6.262 r_scangle_other 6.26 r_mcangle_it 5.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.166 r_dihedral_angle_4_deg 20.044 r_dihedral_angle_3_deg 16.557 r_dihedral_angle_other_3_deg 13.943 r_lrange_it 8.538 r_lrange_other 8.492 r_dihedral_angle_1_deg 7.532 r_scangle_it 6.262 r_scangle_other 6.26 r_mcangle_it 5.092 r_mcangle_other 5.091 r_scbond_it 4.043 r_scbond_other 4.042 r_mcbond_other 3.454 r_mcbond_it 3.453 r_angle_refined_deg 1.87 r_angle_other_deg 1.382 r_chiral_restr_other 1.011 r_symmetry_xyhbond_nbd_other 0.231 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.184 r_nbd_other 0.183 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.161 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2424 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing