3V62

Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52791.9 M AMMONIUM SULFATE 4% PEG 400 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
3.2662.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.817α = 90
b = 62.256β = 135.04
c = 139.247γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0750NSLSX29A

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
12.95099.70.06611.83.810108026583-1
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)
12.92.9599.40.6323.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entries 1PLQ and 1EUV2.95025191134298.830.187020.184230.23656RANDOM88.556
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]
-4.62-3.114.61-4.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.894
r_dihedral_angle_3_deg20.123
r_dihedral_angle_4_deg17.792
r_dihedral_angle_1_deg6.36
r_scangle_it2.989
r_angle_refined_deg1.697
r_scbond_it1.661
r_mcangle_it1.429
r_mcbond_it0.743
r_chiral_restr0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.894
r_dihedral_angle_3_deg20.123
r_dihedral_angle_4_deg17.792
r_dihedral_angle_1_deg6.36
r_scangle_it2.989
r_angle_refined_deg1.697
r_scbond_it1.661
r_mcangle_it1.429
r_mcbond_it0.743
r_chiral_restr0.157
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5616
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
PHASERphasing