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Tandem Tudor and PHD domains of UHRF2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ASK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25% PEG-3350, 0.2 M
NaCl, 0.1 M HEPES pH 7.5, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.28 α = 90 b = 71.28 β = 90 c = 120.052 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 2014-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.2822 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 2.29 50 98.3 0.048 13.8 8.5 14292
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 2.29 2.33 98 0.967 8.8 679
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 3ASK 2.29 50 13552 721 98.53 0.23067 0.22902 0.2381 0.25982 0.2662 RANDOM 81.091
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] -0.73 -0.73 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.506 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 13.12 r_long_range_B_other 5.211 r_long_range_B_refined 5.207 r_dihedral_angle_1_deg 4.923 r_scangle_other 3.091 r_mcangle_it 2.586 r_mcangle_other 2.585 r_scbond_it 2.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.506 r_dihedral_angle_4_deg 17.607 r_dihedral_angle_3_deg 13.12 r_long_range_B_other 5.211 r_long_range_B_refined 5.207 r_dihedral_angle_1_deg 4.923 r_scangle_other 3.091 r_mcangle_it 2.586 r_mcangle_other 2.585 r_scbond_it 2.212 r_scbond_other 2.21 r_mcbond_it 1.541 r_mcbond_other 1.54 r_angle_refined_deg 0.973 r_angle_other_deg 0.676 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1700 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction