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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 2GBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 313 sodium/potassium tartrate, sodium acetate, KCl
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.906 α = 90 b = 94.906 β = 90 c = 276.523 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 2020-04-09 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) 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 2.6 47.5 99.9 0.069 12.5 5.3 28555
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 2.6 2.72 0.612
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 2GBL 2.6 47.5 27082 1465 99.84 0.2819 0.2791 0.2788 0.3366 0.3334 RANDOM 47.208
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] -6.27 -3.13 -6.27 20.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.438 r_dihedral_angle_3_deg 24.243 r_dihedral_angle_4_deg 23.898 r_dihedral_angle_1_deg 3.537 r_angle_other_deg 2.561 r_angle_refined_deg 1.249 r_bond_other_d 0.039 r_chiral_restr 0.03 r_gen_planes_other 0.004 r_bond_refined_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.438 r_dihedral_angle_3_deg 24.243 r_dihedral_angle_4_deg 23.898 r_dihedral_angle_1_deg 3.537 r_angle_other_deg 2.561 r_angle_refined_deg 1.249 r_bond_other_d 0.039 r_chiral_restr 0.03 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6404 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing