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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 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.411 α = 90 b = 159.874 β = 90 c = 207.243 γ = 90
Symmetry Space Group P 21 21 21
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 2016-05-30 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 2.8 30 99.9 0.092 21.4 7.4 75955
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 2.8 2.9 0.751
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 2.8 29.96 63354 3284 87.43 0.2532 0.2498 0.2484 0.3176 0.3125 RANDOM 39.961
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] -0.62 1.05 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_4_deg 22.154 r_dihedral_angle_3_deg 21.915 r_dihedral_angle_1_deg 3.691 r_angle_refined_deg 1.193 r_angle_other_deg 1.122 r_chiral_restr 0.031 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 33.737 r_dihedral_angle_4_deg 22.154 r_dihedral_angle_3_deg 21.915 r_dihedral_angle_1_deg 3.691 r_angle_refined_deg 1.193 r_angle_other_deg 1.122 r_chiral_restr 0.031 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 20506 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 384
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing