5VNA

Crystal structure of human YEATS domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.42901.24 M ammonium sulfate, 100 mM CHES pH 9.4
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.158α = 90
b = 79.926β = 90
c = 121.643γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 225 mm CCD2016-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15099.627.127.240747
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1899.936.6

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 REPLACEMENTTHROUGHOUT3QRL2.148.438396208399.570.176310.173810.22228RANDOM39.951
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]
0.12-0.140.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_4_deg21.122
r_dihedral_angle_3_deg14.422
r_long_range_B_refined8.946
r_long_range_B_other8.855
r_dihedral_angle_1_deg6.925
r_scangle_other6.361
r_mcangle_it5.041
r_mcangle_other5.041
r_scbond_it4.562
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.281
r_dihedral_angle_4_deg21.122
r_dihedral_angle_3_deg14.422
r_long_range_B_refined8.946
r_long_range_B_other8.855
r_dihedral_angle_1_deg6.925
r_scangle_other6.361
r_mcangle_it5.041
r_mcangle_other5.041
r_scbond_it4.562
r_scbond_other4.561
r_mcbond_other3.508
r_mcbond_it3.507
r_angle_refined_deg1.957
r_angle_other_deg1.038
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4205
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing