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Crystal structure of D1050E mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.05 290.15 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05
Crystal Properties Matthews coefficient Solvent content 2.44 49.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.337 α = 90 b = 98.728 β = 90 c = 79.897 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 225 mm CCD 2009-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.975220 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 47.6 99.2 0.117 10.8 5.7 15893
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 1.95 2.06 94.8 0.665 1.6 4
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 3MM4 1.95 42.37 13110 696 86.12 0.20848 0.20718 0.216 0.23381 0.2393 RANDOM 34.402
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] 1.17 0.05 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.111 r_dihedral_angle_4_deg 17.502 r_dihedral_angle_3_deg 16.352 r_long_range_B_refined 9.004 r_long_range_B_other 8.974 r_scangle_other 7.339 r_dihedral_angle_1_deg 6.629 r_mcangle_it 4.722 r_mcangle_other 4.719 r_scbond_it 4.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.111 r_dihedral_angle_4_deg 17.502 r_dihedral_angle_3_deg 16.352 r_long_range_B_refined 9.004 r_long_range_B_other 8.974 r_scangle_other 7.339 r_dihedral_angle_1_deg 6.629 r_mcangle_it 4.722 r_mcangle_other 4.719 r_scbond_it 4.702 r_scbond_other 4.698 r_mcbond_it 3.302 r_mcbond_other 3.285 r_angle_refined_deg 2.037 r_angle_other_deg 1.625 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing