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Crystal Structure of the two MBT repeats from Sex-Comb on Midleg (SCM) in Complex with Di-Methyl Lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.3 293 15% (w/v) PEG3350, 100 mM calcium acetate and 3% ethanol, pH 7.3, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.12 α = 90 b = 83.12 β = 90 c = 75.768 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315 2006-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.934 ESRF ID29
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 20.8 96.1 0.0456 6.5 9.4 17807 1 1
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 2.1 81.1 0.364 1.7 7.1
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 (All) 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 2R57 2 20.8 16819 907 96.19 0.18803 0.18803 0.18596 0.1868 0.22875 0.2339 RANDOM 36.647
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] 0.83 0.83 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.56 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 15.035 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.297 r_scbond_it 1.563 r_angle_refined_deg 1.222 r_mcangle_it 1.043 r_mcbond_it 0.655 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.56 r_dihedral_angle_4_deg 17.248 r_dihedral_angle_3_deg 15.035 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.297 r_scbond_it 1.563 r_angle_refined_deg 1.222 r_mcangle_it 1.043 r_mcbond_it 0.655 r_nbtor_refined 0.302 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1661 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DNA data collection XDS data reduction XSCALE data scaling PHASER phasing