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Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), orthorhombic form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQW PDB entry 2PQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 300 6% PEG 3350, 0.1M Ammonium sulfate, 20% Glycerol, 0.1 M Sodium acetate pH 4.4 , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.894 α = 90 b = 124.64 β = 90 c = 90.031 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS varimax 2006-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.54000
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 1.86 37.48 0.085 6.6 103400 103400
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PQW 1.86 37.48 98168 5159 98.95 0.19292 0.19086 0.1891 0.23131 0.2302 RANDOM 26.538
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] 0.05 0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.879 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 13.863 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.473 r_scbond_it 2.323 r_mcangle_it 1.555 r_angle_refined_deg 1.444 r_mcbond_it 1.006 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.879 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 13.863 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.473 r_scbond_it 2.323 r_mcangle_it 1.555 r_angle_refined_deg 1.444 r_mcbond_it 1.006 r_nbtor_refined 0.305 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.194 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 7746 Nucleic Acid Atoms Solvent Atoms 950 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing