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Crystal Structure of Circadian Clock Protein KaiA from Synechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M2E PDB ENTRY 1M2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 Ammonium Sulfate, Sodium Cacodylate, PEG 8000, Glycerol, pH 6.5, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.111 α = 90 b = 125.818 β = 114.9 c = 56.818 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 95.2 0.04 0.04 30.6 3.6 38494
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 54.3 0.362 0.362 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION combination of SAD phasing, real space molecular replacement, ARP/wARP phase improvement, and non-crystallographic symmetry averaging THROUGHOUT PDB ENTRY 1M2E 2.03 20 36552 1905 98.92 0.21306 0.21012 0.27144 0.2636 RANDOM 39.112
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] -0.39 1.54 -0.36 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.389 r_scangle_it 2.928 r_scbond_it 1.745 r_mcangle_it 1.436 r_angle_refined_deg 1.116 r_mcbond_it 0.756 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.389 r_scangle_it 2.928 r_scbond_it 1.745 r_mcangle_it 1.436 r_angle_refined_deg 1.116 r_mcbond_it 0.756 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4331 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing