2VWB

Structure of the archaeal Kae1-Bud32 fusion protein MJ1130: a model for the eukaryotic EKC-KEOPS subcomplex involved in transcription and telomere homeostasis.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IVNPDB ENTRY 1IVN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.1 M SODIUM CITRATE, 5-10% ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.850

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.418α = 90
b = 148.948β = 90
c = 65.118γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-03-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.052094.70.112.4526424-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.2196.20.562.85.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTPDB ENTRY 1IVN3.0519.9525085131994.40.2240.220.301RANDOM60.94
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]
-1.54-0.922.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.367
r_dihedral_angle_3_deg22.373
r_dihedral_angle_4_deg21.04
r_dihedral_angle_1_deg6.818
r_scangle_it1.869
r_angle_refined_deg1.478
r_scbond_it1.104
r_mcangle_it0.95
r_mcbond_it0.54
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.367
r_dihedral_angle_3_deg22.373
r_dihedral_angle_4_deg21.04
r_dihedral_angle_1_deg6.818
r_scangle_it1.869
r_angle_refined_deg1.478
r_scbond_it1.104
r_mcangle_it0.95
r_mcbond_it0.54
r_nbtor_refined0.313
r_nbd_refined0.241
r_symmetry_vdw_refined0.217
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.115
r_chiral_restr0.102
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms8148
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing