☰ Navigation Tabs
The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R3A PDB ENTRY 2R3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1 uL protein (1:10 molar ratio of SETD2:AdoMet) + 1 uL reservoir solution (30% PEG2000 MME, 0.1 M potassium thiocyanate), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.293 α = 90 b = 76.663 β = 90 c = 78.093 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 315r 2009-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 1.991 50 98.9 0.101 8.3 6.9 21811
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 1.991 2.03 90.7 0.753 2.9
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 2R3A 2.06 38.36 18905 1011 99.41 0.20953 0.20741 0.207 0.24904 0.2483 RANDOM 39.608
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] 5.62 -4.55 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.318 r_dihedral_angle_4_deg 19.05 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 5.63 r_angle_refined_deg 1.251 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.318 r_dihedral_angle_4_deg 19.05 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 5.63 r_angle_refined_deg 1.251 r_chiral_restr 0.085 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_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 30
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing