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Crystal Structure of Designed 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 VAPOR DIFFUSION 313 Acetic acid
Sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.126 α = 90 b = 385.574 β = 113.15 c = 108.115 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 PIXEL DECTRIS EIGER X 16M 2024-02-16 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 49.35 99.9 0.12 12.4 7 138997
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 3.11 1.09
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 49.35 119652 6294 99.82 0.28262 0.28017 0.2775 0.32907 0.3221 RANDOM 67.435
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] -1.28 0.75 -0.47 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.694 r_dihedral_angle_2_deg 4.89 r_dihedral_angle_1_deg 4.493 r_long_range_B_refined 4.199 r_long_range_B_other 4.196 r_mcangle_it 2.332 r_mcangle_other 2.332 r_scangle_other 1.648 r_mcbond_it 1.271 r_mcbond_other 1.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.694 r_dihedral_angle_2_deg 4.89 r_dihedral_angle_1_deg 4.493 r_long_range_B_refined 4.199 r_long_range_B_other 4.196 r_mcangle_it 2.332 r_mcangle_other 2.332 r_scangle_other 1.648 r_mcbond_it 1.271 r_mcbond_other 1.271 r_scbond_it 0.845 r_scbond_other 0.845 r_angle_refined_deg 0.61 r_angle_other_deg 0.244 r_chiral_restr 0.027 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36026 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 672
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing