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Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 291 23% PEG3350, 0.1 M HEPES-Na, 5% MPD, 0.2 M NaCl, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.96 37.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.528 α = 104.55 b = 46.259 β = 93.87 c = 58.307 γ = 90.08
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 IV 2010-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 20 93 0.061 24.5256 3.5 16102 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 68.4 0.268 3.73 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 3CLZ 2.3 19.73 15216 814 92.97 0.18682 0.18432 0.23387 0.2169 RANDOM 37.908
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] -2.87 -0.38 0.26 0.59 0.49 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.57 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 15.657 r_dihedral_angle_1_deg 5.159 r_scangle_it 1.478 r_angle_refined_deg 1.079 r_scbond_it 0.876 r_mcangle_it 0.537 r_mcbond_it 0.285 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.57 r_dihedral_angle_4_deg 18.191 r_dihedral_angle_3_deg 15.657 r_dihedral_angle_1_deg 5.159 r_scangle_it 1.478 r_angle_refined_deg 1.079 r_scbond_it 0.876 r_mcangle_it 0.537 r_mcbond_it 0.285 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling