4I51

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HNAPDB entry 3HNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510% ISOPROPANOL, 20% PEG4000; 0.1M HEPES PH7.5, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 297K
Crystal Properties
Matthews coefficientSolvent content
2.4349.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.497α = 90
b = 83.8β = 90
c = 95.052γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97958APS23-ID-B

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
11.95098.60.07210.57.95241725.2
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)
11.91.93830.5615.2

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 REPLACEMENTTHROUGHOUTPDB entry 3HNA1.941.7852354107598.50.1710.1710.195RANDOM33.11
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]
0.550.37-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.682
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg13.347
r_dihedral_angle_1_deg6.945
r_angle_refined_deg1.163
r_chiral_restr0.095
r_gen_planes_refined0.011
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.682
r_dihedral_angle_4_deg16.898
r_dihedral_angle_3_deg13.347
r_dihedral_angle_1_deg6.945
r_angle_refined_deg1.163
r_chiral_restr0.095
r_gen_planes_refined0.011
r_bond_refined_d0.008
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4298
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms87

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling