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Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 ammonium sulfate, potassium chloride, Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.66 66.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.829 α = 90 b = 210.829 β = 90 c = 156.421 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 IMAGE PLATE RIGAKU RAXIS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 100 96.2 0.117 12.4 4 148110 148110 13.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 89.7 0.304 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1Q2V 2.3 41.97 148077 148077 7449 96.1 0.213 0.213 0.2684 0.25 0.2904 RANDOM 25.7
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] -2.45 -2.45 4.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scangle_it 3.79 c_scbond_it 2.54 c_mcangle_it 2.28 c_mcbond_it 1.4 c_angle_deg 1.3 c_improper_angle_d 0.77 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scangle_it 3.79 c_scbond_it 2.54 c_mcangle_it 2.28 c_mcbond_it 1.4 c_angle_deg 1.3 c_improper_angle_d 0.77 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15788 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 128
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing