5D5W

Crystal structure of Chaetomium thermophilum Skn7 with HSE DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HTS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29311 % PEG-3350, 0.18 M tri-Ammonium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.771α = 90
b = 78.397β = 90
c = 90.084γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97702ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.34945.04298.90.0450.0510.02317.44.76090609061.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.3492.4899.20.9580.9580.4690.84.8870

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 REPLACEMENTTHROUGHOUT3HTS2.3530579128098.60.21730.21540.2501RANDOM72.272
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]
-6.224.61.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.317
r_dihedral_angle_3_deg17.2
r_dihedral_angle_4_deg11.042
r_dihedral_angle_1_deg6.563
r_angle_other_deg1.397
r_angle_refined_deg1.044
r_chiral_restr0.103
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.317
r_dihedral_angle_3_deg17.2
r_dihedral_angle_4_deg11.042
r_dihedral_angle_1_deg6.563
r_angle_other_deg1.397
r_angle_refined_deg1.044
r_chiral_restr0.103
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms816
Nucleic Acid Atoms243
Solvent Atoms22
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction