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Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 9% ethanol, 100mM imidazole pH7.6, 200mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.655 α = 90 b = 51.807 β = 122.83 c = 97.468 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU JUPITER 210 2005-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.97905, 0.97934 SPring-8 BL38B1
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 50 95.5 0.083 26.462 6.8 46906
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) 2 2.07 73.4 0.509 4.2 3572
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.07 15 43605 2195 97.63 0.199 0.197 0.2106 0.25 RANDOM 33.96
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] -1.08 0.56 -0.72 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.587 r_scangle_it 4.941 r_scbond_it 2.979 r_mcangle_it 1.997 r_angle_refined_deg 1.87 r_mcbond_it 1.111 r_angle_other_deg 0.953 r_symmetry_vdw_other 0.3 r_nbd_other 0.244 r_nbd_refined 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.587 r_scangle_it 4.941 r_scbond_it 2.979 r_mcangle_it 1.997 r_angle_refined_deg 1.87 r_mcbond_it 1.111 r_angle_other_deg 0.953 r_symmetry_vdw_other 0.3 r_nbd_other 0.244 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.116 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.074 r_bond_refined_d 0.022 r_symmetry_hbond_refined 0.017 r_metal_ion_refined 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5270 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 84
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction