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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 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.191 α = 90 b = 95.191 β = 90 c = 184.086 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 2020-07-24 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 2.93 49.22 99.7 0.117 15.8 10.3 20257
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 2.93 3.03 0.913
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 2.93 49.22 19328 939 99.79 0.2783 0.2755 0.2753 0.3351 0.3214 RANDOM 71.374
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] -4.57 -2.28 -4.57 14.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.985 r_dihedral_angle_3_deg 25.469 r_dihedral_angle_4_deg 22.097 r_dihedral_angle_1_deg 2.944 r_angle_refined_deg 1.234 r_angle_other_deg 1.123 r_chiral_restr 0.029 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.985 r_dihedral_angle_3_deg 25.469 r_dihedral_angle_4_deg 22.097 r_dihedral_angle_1_deg 2.944 r_angle_refined_deg 1.234 r_angle_other_deg 1.123 r_chiral_restr 0.029 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6510 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing