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Crystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis (crystal form 3).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M Bis-Tri pH 6.5, 0.1 M NaCl, 1.5 M (NH4)2SO4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.523 α = 90 b = 31.523 β = 90 c = 81.599 γ = 90
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 2M-F 2016-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000040 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.85 31.523 99.8 0.073 1 21.4 13.5 6769 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.97 99.3 2.76 0.4 1
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 6TO5 1.853 31.5 6767 334 99.882 0.211 0.2087 0.2146 0.265 0.2668 38.292
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] 7.702 7.702 -15.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 28.606 r_dihedral_angle_2_deg 28.527 r_dihedral_angle_3_deg 16.136 r_lrange_other 6.667 r_lrange_it 6.662 r_scangle_other 5.094 r_scangle_it 5.093 r_dihedral_angle_1_deg 3.575 r_scbond_it 3.247 r_scbond_other 3.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 28.606 r_dihedral_angle_2_deg 28.527 r_dihedral_angle_3_deg 16.136 r_lrange_other 6.667 r_lrange_it 6.662 r_scangle_other 5.094 r_scangle_it 5.093 r_dihedral_angle_1_deg 3.575 r_scbond_it 3.247 r_scbond_other 3.244 r_mcangle_it 3.084 r_mcangle_other 3.084 r_mcbond_it 2.073 r_mcbond_other 2.064 r_angle_other_deg 1.23 r_angle_refined_deg 1.2 r_symmetry_xyhbond_nbd_refined 0.338 r_xyhbond_nbd_refined 0.273 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.21 r_nbd_other 0.193 r_xyhbond_nbd_other 0.191 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.149 r_ncsr_local_group_1 0.131 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 743 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing