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Plant peptide hormone receptor H1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 0.2 M ammonium sulfate
0.1 M citric acid pH 4.0
30% w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 3.57 65.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.539 α = 99.178 b = 84.001 β = 113.727 c = 89.061 γ = 108.41
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 2019-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000033 SLS X06DA
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 1.83 47.084 97.4 0.042 0.06 0.042 0.999 10.3 3.5 158310
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 1.83 1.86 0.59 0.834 0.59 0.721 3.6
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 5IXO 1.83 47.08 158310 8013 97.392 0.205 0.2044 0.2125 0.2164 0.2255 29.287
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] -0.733 -0.079 -0.127 1.131 -1.075 0.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.24 r_dihedral_angle_other_1_deg 34.523 r_dihedral_angle_4_deg 13.785 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 4.774 r_lrange_it 3.375 r_lrange_other 3.363 r_scangle_it 1.669 r_scangle_other 1.669 r_angle_other_deg 1.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.24 r_dihedral_angle_other_1_deg 34.523 r_dihedral_angle_4_deg 13.785 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_1_deg 4.774 r_lrange_it 3.375 r_lrange_other 3.363 r_scangle_it 1.669 r_scangle_other 1.669 r_angle_other_deg 1.283 r_scbond_it 1.205 r_scbond_other 1.205 r_mcangle_it 1.201 r_mcangle_other 1.201 r_angle_refined_deg 1.102 r_mcbond_it 0.674 r_mcbond_other 0.674 r_symmetry_metal_ion_refined 0.418 r_symmetry_nbd_refined 0.231 r_nbd_other 0.21 r_symmetry_nbd_other 0.18 r_nbd_refined 0.179 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.129 r_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.086 r_ext_dist_refined_d 0.076 r_chiral_restr 0.046 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8798 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 643
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Coot model building PHASER phasing