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PAS-GAF bidomain of Glycine max phytochromeA
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, HANGING DROP 6.5 283.15 0.05 M imidazole, 0.05 M MES, 0.02 M DL-Glutamatic acid monohydrate, 0.02 M DL-Alanine, 0.02M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine, 12% (v/v) Glycerol, 6% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.423 α = 90 b = 113.233 β = 93.521 c = 68.457 γ = 90
Symmetry Space Group P 1 21 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 PSI PILATUS 6M 2019-10-19 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 2.13 44.35 99.5 0.127 0.151 0.08 0.998 10 6.8 46863 36.395
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 2.13 2.19 99.8 1.95 2.306 0.875 0.318 0.9 6.9
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 6TBY 2.13 44.347 46830 1866 99.399 0.191 0.1892 0.1953 0.2415 0.2487 48.593
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] 0.226 0.067 -0.05 -0.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.513 r_dihedral_angle_4_deg 20.255 r_dihedral_angle_3_deg 18.163 r_lrange_it 10.14 r_lrange_other 10.131 r_dihedral_angle_1_deg 8.109 r_scangle_it 7.249 r_scangle_other 7.249 r_mcangle_it 5.693 r_mcangle_other 5.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.513 r_dihedral_angle_4_deg 20.255 r_dihedral_angle_3_deg 18.163 r_lrange_it 10.14 r_lrange_other 10.131 r_dihedral_angle_1_deg 8.109 r_scangle_it 7.249 r_scangle_other 7.249 r_mcangle_it 5.693 r_mcangle_other 5.692 r_scbond_it 4.856 r_scbond_other 4.855 r_mcbond_it 3.705 r_mcbond_other 3.704 r_dihedral_angle_other_3_deg 3.479 r_angle_refined_deg 2.469 r_angle_other_deg 1.663 r_chiral_restr_other 1.141 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.215 r_nbd_other 0.2 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.136 r_chiral_restr 0.124 r_symmetry_nbtor_other 0.096 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4982 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing