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Crystal structure of Orobanche minor KAI2d4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M sodium acetate pH 4.5, 0.8 M di-ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.448 α = 90 b = 97.448 β = 90 c = 147.668 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2020-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000 ALS 8.2.1
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 2.3 48.72 99.96 0.989 8.03 21.6 32317 20.69
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 2.3 2.382 100 0.744 20.7
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 4JYP 2.3 48.72 1.33 32311 1688 99.98 0.179 0.1761 0.1754 0.232 0.2313 22.95
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 11.3766 f_angle_d 0.6453 f_chiral_restr 0.0471 f_plane_restr 0.0055 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4168 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing