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Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OZ2 PDB entry 1OZ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 300 0.1M Sodium acetate pH 4.6, 4% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 4.66 73.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.013 α = 90 b = 117.013 β = 90 c = 90.38 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2007-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.10000 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 33.79 99.1 0.067 12.5 5.1 48125 48125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 96.9 0.718 1.4 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1OZ2 2 33.79 45655 45655 2430 99.09 0.19661 0.1949 0.1915 0.22804 0.2217 RANDOM 34.94
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.207 r_dihedral_angle_4_deg 23.985 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.75 r_scangle_it 3.135 r_scbond_it 2.122 r_angle_refined_deg 1.415 r_mcangle_it 1.397 r_mcbond_it 0.884 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.207 r_dihedral_angle_4_deg 23.985 r_dihedral_angle_3_deg 15.11 r_dihedral_angle_1_deg 6.75 r_scangle_it 3.135 r_scbond_it 2.122 r_angle_refined_deg 1.415 r_mcangle_it 1.397 r_mcbond_it 0.884 r_nbtor_refined 0.303 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 2636 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction HKL-2000 data scaling MOLREP phasing