6Y39

HapE-P88L mutant CCAAT-binding complex from Aspergillus nidulans with cycA DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G92 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293175 mM di-ammonium phosphate, 19% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.0759.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.15α = 90
b = 103.5β = 90
c = 159.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.349980.0710.55.152851
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)
12.32.40.598

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 REPLACEMENTTHROUGHOUT4G922.33050185264197.950.22250.22090.254RANDOM68.217
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]
-1.223.87-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.887
r_dihedral_angle_3_deg16.31
r_dihedral_angle_4_deg15.267
r_dihedral_angle_1_deg5.603
r_angle_refined_deg1.331
r_angle_other_deg1.262
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.887
r_dihedral_angle_3_deg16.31
r_dihedral_angle_4_deg15.267
r_dihedral_angle_1_deg5.603
r_angle_refined_deg1.331
r_angle_other_deg1.262
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5725
Nucleic Acid Atoms1025
Solvent Atoms59
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing