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Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 12-30), orthorhombic form I
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 5 300 5% PEG 4000, 0.1M Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.458 α = 90 b = 117.809 β = 90 c = 132.316 γ = 90
Symmetry Space Group P 21 21 21
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 2007-01-10 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 2.05 39.65 97.4 0.082 4.7 86421 86421
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2PQW 2.05 39.65 81955 81955 4370 97.34 0.18142 0.18142 0.1791 0.22533 0.2401 RANDOM 27.404
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] -0.2 0.06 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 24.206 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 6.937 r_scangle_it 4.09 r_scbond_it 2.706 r_angle_refined_deg 1.727 r_mcangle_it 1.656 r_mcbond_it 1.1 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.335 r_dihedral_angle_4_deg 24.206 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 6.937 r_scangle_it 4.09 r_scbond_it 2.706 r_angle_refined_deg 1.727 r_mcangle_it 1.656 r_mcbond_it 1.1 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.207 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.12 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 7840 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing