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Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 300 20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.42 49.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.526 α = 90 b = 83.372 β = 90 c = 95.13 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 CCD ADSC QUANTUM 315 v 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 100 96.5 0.07 0.07 12 5 101405 101405
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2RFI 1.5 62.75 101405 101405 5324 99.99 0.16738 0.16738 0.16604 0.165 0.19273 0.1913 RANDOM 17.872
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] -0.11 0.18 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.808 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.833 r_scangle_it 3.069 r_scbond_it 2.005 r_mcangle_it 1.374 r_angle_refined_deg 1.285 r_mcbond_it 0.859 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.808 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 5.833 r_scangle_it 3.069 r_scbond_it 2.005 r_mcangle_it 1.374 r_angle_refined_deg 1.285 r_mcbond_it 0.859 r_nbtor_refined 0.308 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4492 Nucleic Acid Atoms Solvent Atoms 888 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling