2PQW

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.63000.1M Sodium acetate pH 4.6, 4% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
4.6673.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.013α = 90
b = 117.013β = 90
c = 90.38γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.10000NSLSX29A

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
1233.7999.10.06712.55.14812548125
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)
122.0596.90.7181.44.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1OZ2233.794565545655243099.090.196610.19490.22804RANDOM34.94
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.207
r_dihedral_angle_4_deg23.985
r_dihedral_angle_3_deg15.11
r_dihedral_angle_1_deg6.75
r_scangle_it3.135
r_scbond_it2.122
r_angle_refined_deg1.415
r_mcangle_it1.397
r_mcbond_it0.884
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.207
r_dihedral_angle_4_deg23.985
r_dihedral_angle_3_deg15.11
r_dihedral_angle_1_deg6.75
r_scangle_it3.135
r_scbond_it2.122
r_angle_refined_deg1.415
r_mcangle_it1.397
r_mcbond_it0.884
r_nbtor_refined0.303
r_nbd_refined0.198
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.128
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2636
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing