3IHO

The C-terminal glycosylase domain of human MBD4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.525% PEG3350, 0.2M Li Sulfate, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.9958.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.541α = 90
b = 83.541β = 90
c = 73.956γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
12.69751.7193.70.096.33.75287
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)
12.6972.864.30.3152.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.751.71458921890.850.187350.182480.29003RANDOM24.405
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]
1.890.941.89-2.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.271
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg18.877
r_dihedral_angle_1_deg6.489
r_scangle_it4.228
r_scbond_it2.544
r_angle_refined_deg1.978
r_mcangle_it1.61
r_mcbond_it0.804
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.271
r_dihedral_angle_4_deg18.907
r_dihedral_angle_3_deg18.877
r_dihedral_angle_1_deg6.489
r_scangle_it4.228
r_scbond_it2.544
r_angle_refined_deg1.978
r_mcangle_it1.61
r_mcbond_it0.804
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.01
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 Atoms1146
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction