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Crystal structure of Striga KAI2-like protein in complex with karrikin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 Sodium formate, Tris
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.757 α = 90 b = 75.757 β = 90 c = 181.266 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.2 19.7 99.9 97.8 20.6 96642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 99.6 0.39 5.3 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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5DNW 1.2 19.7 91454 4887 99.8 0.14089 0.14009 0.1399 0.15539 0.156 RANDOM 22.067
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.709 r_sphericity_free 30.658 r_dihedral_angle_4_deg 18.496 r_sphericity_bonded 12.863 r_dihedral_angle_3_deg 12.698 r_dihedral_angle_1_deg 6.256 r_long_range_B_refined 3.501 r_long_range_B_other 3.5 r_mcangle_other 2.673 r_mcangle_it 2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.709 r_sphericity_free 30.658 r_dihedral_angle_4_deg 18.496 r_sphericity_bonded 12.863 r_dihedral_angle_3_deg 12.698 r_dihedral_angle_1_deg 6.256 r_long_range_B_refined 3.501 r_long_range_B_other 3.5 r_mcangle_other 2.673 r_mcangle_it 2.666 r_scangle_other 2.665 r_scbond_it 2.274 r_scbond_other 2.273 r_mcbond_other 2.24 r_mcbond_it 2.239 r_rigid_bond_restr 2.143 r_angle_refined_deg 1.692 r_angle_other_deg 1.057 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2076 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing