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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/pottasium tartrae, sodium acetate, KCl
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.323 α = 90 b = 94.323 β = 90 c = 180.586 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) 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 2.64 48.51 99.9 0.97 13.2 10.5 26712
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 2.64 2.77 0.899
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 2.64 48.51 25305 1339 99.76 0.2957 0.2939 0.293 0.3306 0.3294 RANDOM 59.847
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] -4.95 -2.48 -4.95 16.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_3_deg 23.851 r_dihedral_angle_4_deg 21.453 r_dihedral_angle_1_deg 2.968 r_angle_refined_deg 1.213 r_angle_other_deg 1.138 r_chiral_restr 0.028 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.841 r_dihedral_angle_3_deg 23.851 r_dihedral_angle_4_deg 21.453 r_dihedral_angle_1_deg 2.968 r_angle_refined_deg 1.213 r_angle_other_deg 1.138 r_chiral_restr 0.028 r_bond_refined_d 0.002 r_gen_planes_refined 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 6510 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing