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Structure of the archaeal Kae1-Bud32 fusion protein MJ1130: a model for the eukaryotic EKC-KEOPS subcomplex involved in transcription and telomere homeostasis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IVN PDB ENTRY 1IVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.1 M SODIUM CITRATE, 5-10% ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.8 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.418 α = 90 b = 148.948 β = 90 c = 65.118 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC CCD 2006-03-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.05 20 94.7 0.1 12.4 5 26424 -3
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 3.05 3.21 96.2 0.56 2.8 5.1
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 SAD THROUGHOUT PDB ENTRY 1IVN 3.05 19.95 25085 1319 94.4 0.224 0.22 0.2098 0.301 0.286 RANDOM 60.94
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] -1.54 -0.92 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.367 r_dihedral_angle_3_deg 22.373 r_dihedral_angle_4_deg 21.04 r_dihedral_angle_1_deg 6.818 r_scangle_it 1.869 r_angle_refined_deg 1.478 r_scbond_it 1.104 r_mcangle_it 0.95 r_mcbond_it 0.54 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.367 r_dihedral_angle_3_deg 22.373 r_dihedral_angle_4_deg 21.04 r_dihedral_angle_1_deg 6.818 r_scangle_it 1.869 r_angle_refined_deg 1.478 r_scbond_it 1.104 r_mcangle_it 0.95 r_mcbond_it 0.54 r_nbtor_refined 0.313 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.217 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8148 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing