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Crystal Structure of KAI2 from Oryza sativa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M Sodium HEPES, 0.1M MOPS (acid) pH 7.5, 0.018M Magnesium chloride hexahydrate, 0.018M Calcium chloride dihydrate, 9.4% v/v MPD, 9.4% v/v PEG 1000, 9.4% v/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.636 α = 90 b = 85.385 β = 114.91 c = 44.62 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS EIGER X 9M 2021-12-01 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) R Sym I (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 1.68 42.73 93.8 0.069 16 3.5 27040
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 84.1 0.422 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.68 42.73 25611 1428 93.36 0.16949 0.16791 0.1813 0.1975 0.1787 RANDOM 21.166
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] -0.18 0.14 2.69 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.319 r_long_range_B_refined 5.909 r_long_range_B_other 5.868 r_dihedral_angle_1_deg 5.634 r_scangle_other 4.909 r_dihedral_angle_2_deg 4.231 r_scbond_it 3.157 r_scbond_other 3.155 r_mcangle_it 2.751 r_mcangle_other 2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.319 r_long_range_B_refined 5.909 r_long_range_B_other 5.868 r_dihedral_angle_1_deg 5.634 r_scangle_other 4.909 r_dihedral_angle_2_deg 4.231 r_scbond_it 3.157 r_scbond_other 3.155 r_mcangle_it 2.751 r_mcangle_other 2.75 r_mcbond_it 1.919 r_mcbond_other 1.913 r_angle_refined_deg 1.553 r_angle_other_deg 0.504 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2067 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing