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PAS-GAF bidomain of Glycine max phytochrome A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 0.12 M Ethylene glycols (0.3M diethylene glycol; 0.3M triethylene glycol; 0.3M tetraethylene glycol; 0.3M pentaethylene glycol), 0.1 M Tris (base);BICINE pH 8.5, 30% v/v Precipitant Mix 1 (20% v/v PEG 500 MME; 10 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.287 α = 90 b = 111.812 β = 92.308 c = 68.273 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 40 PIXEL DECTRIS PILATUS 6M 2021-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.896 BESSY 14.3
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 1.58 43.841 99.58 0.998 12.84 3.7 112709
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 1.58 1.636 0.418
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.58 43.841 112680 5372 99.614 0.176 0.175 0.1858 0.1945 0.2031 28.817
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] -0.064 0.128 0.004 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.062 r_dihedral_angle_6_deg 15.482 r_lrange_it 9.361 r_lrange_other 9.309 r_dihedral_angle_2_deg 8.465 r_dihedral_angle_1_deg 6.537 r_scangle_it 6.258 r_scangle_other 6.257 r_mcangle_it 4.613 r_mcangle_other 4.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.062 r_dihedral_angle_6_deg 15.482 r_lrange_it 9.361 r_lrange_other 9.309 r_dihedral_angle_2_deg 8.465 r_dihedral_angle_1_deg 6.537 r_scangle_it 6.258 r_scangle_other 6.257 r_mcangle_it 4.613 r_mcangle_other 4.613 r_scbond_other 4.038 r_scbond_it 4.037 r_mcbond_it 2.884 r_mcbond_other 2.882 r_angle_refined_deg 1.623 r_angle_other_deg 0.526 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.232 r_nbd_other 0.226 r_symmetry_xyhbond_nbd_refined 0.222 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_other 0.087 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4924 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing