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Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 313 sodium/pottasium tartrae, sodium acetate, KCl
Crystal Properties Matthews coefficient Solvent content 1.97 37.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.188 α = 90 b = 94.188 β = 90 c = 179.168 γ = 120
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 EIGER X 16M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.729 47.4 99.8 0.998 14.9 10.7 23865
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 2.729 2.73 0.998 11
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 (All) 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 2.729 47.138 23864 1109 99.695 0.283 0.28 0.2796 0.338 0.3262 RANDOM 61.884
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] -5.822 -2.911 -5.822 18.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.988 r_dihedral_angle_6_deg 12.844 r_lrange_it 4.996 r_lrange_other 4.995 r_dihedral_angle_2_deg 3.303 r_dihedral_angle_1_deg 3.29 r_mcangle_other 2.863 r_mcangle_it 2.862 r_scangle_it 2.182 r_scangle_other 2.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.988 r_dihedral_angle_6_deg 12.844 r_lrange_it 4.996 r_lrange_other 4.995 r_dihedral_angle_2_deg 3.303 r_dihedral_angle_1_deg 3.29 r_mcangle_other 2.863 r_mcangle_it 2.862 r_scangle_it 2.182 r_scangle_other 2.181 r_mcbond_it 1.632 r_mcbond_other 1.63 r_scbond_it 1.201 r_scbond_other 1.201 r_angle_refined_deg 0.668 r_dihedral_angle_other_2_deg 0.535 r_symmetry_xyhbond_nbd_refined 0.288 r_angle_other_deg 0.272 r_symmetry_nbd_other 0.211 r_symmetry_nbd_refined 0.207 r_nbd_other 0.203 r_nbd_refined 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.134 r_symmetry_xyhbond_nbd_other 0.089 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6407 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing