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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 313 sodium/pottasium tartrae, sodium acetate, KCl
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.261 α = 90 b = 95.261 β = 90 c = 182.682 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 2.84 47.6 99.4 0.085 12.2 5.4 43729
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 2.84 3.01 0.915
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 7DYJ 2.84 46.13 21166 1035 99.78 0.2852 0.2832 0.286 0.3251 0.3172 RANDOM 69.253
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] -3.25 -1.63 -3.25 10.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_3_deg 24.147 r_dihedral_angle_4_deg 23.911 r_dihedral_angle_1_deg 2.752 r_angle_refined_deg 1.214 r_angle_other_deg 1.135 r_chiral_restr 0.027 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.209 r_dihedral_angle_3_deg 24.147 r_dihedral_angle_4_deg 23.911 r_dihedral_angle_1_deg 2.752 r_angle_refined_deg 1.214 r_angle_other_deg 1.135 r_chiral_restr 0.027 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6537 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing