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Photosensory module (PAS-GAF-PHY) of Glycine max phyB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283.15 200mM MES, 200mM KSCN, 200mM LiCl2, 1% w/v gamma-PGA, 3% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 5.63 78.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.269 α = 90 b = 102.269 β = 90 c = 222.918 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 PILATUS 6M 2019-11-23 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 2.9 47.17 99.9 0.238 0.251 0.077 0.999 12.1 19.8 30704 85.72
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 2.9 3.06 99.9 5.838 6.14 1.893 0.591 0.8 19.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4OUR 2.9 47.17 1.34 30475 1550 99.19 0.2582 0.257 0.2592 0.2824 0.2836 121.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.3242 f_angle_d 1.3917 f_chiral_restr 0.0668 f_bond_d 0.0094 f_plane_restr 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3789 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing