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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 5 313 Acetatic acid, Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.492 α = 90 b = 205.803 β = 115.14 c = 186.177 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2016-10-07 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) 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 3.1 50 99.9 0.102 13.8 3.9 228464
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 3.1 3.15 0.744
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 3.1 49.22 204692 10614 93.67 0.2777 0.2745 0.2721 0.3397 0.335 RANDOM 48.304
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] -0.85 -0.61 0.26 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.605 r_dihedral_angle_3_deg 21.053 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_1_deg 5.769 r_angle_refined_deg 1.496 r_angle_other_deg 1.302 r_chiral_restr 0.04 r_bond_other_d 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.605 r_dihedral_angle_3_deg 21.053 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_1_deg 5.769 r_angle_refined_deg 1.496 r_angle_other_deg 1.302 r_chiral_restr 0.04 r_bond_other_d 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 77135 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 1512
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing