3K26 | pdb_00003k26

Complex structure of EED and trimethylated H3K4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52913.5M NaF, 10 mM TCEP, 15%Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.92α = 90
b = 85.31β = 90
c = 91.39γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

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
11.5848.946.958074

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5819.815807430571000.1640.162290.16440.196590.1973RANDOM15.461
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.721
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg13.461
r_dihedral_angle_1_deg7.084
r_scangle_it6.17
r_scbond_it3.92
r_mcangle_it2.66
r_angle_refined_deg2.409
r_mcbond_it1.586
r_chiral_restr0.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.721
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg13.461
r_dihedral_angle_1_deg7.084
r_scangle_it6.17
r_scbond_it3.92
r_mcangle_it2.66
r_angle_refined_deg2.409
r_mcbond_it1.586
r_chiral_restr0.211
r_bond_refined_d0.031
r_gen_planes_refined0.016
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 Atoms2937
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement