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Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Potassium thiocyanate, 30% PEG MME2000
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.94 α = 90 b = 75.72 β = 90 c = 96.48 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2023-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9792 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.6 19.95 99.8 0.038 0.042 0.017 0.999 21 6.2 34602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 98.3 0.321 0.361 0.162 0.913 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 19.95 32780 1794 99.79 0.15307 0.15228 0.1615 0.16803 0.1727 RANDOM 29.975
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] 0.01 -0.21 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.543 r_dihedral_angle_2_deg 9.729 r_long_range_B_refined 6.321 r_long_range_B_other 6.32 r_dihedral_angle_1_deg 5.281 r_scangle_other 3.885 r_scbond_other 2.688 r_scbond_it 2.687 r_mcangle_it 2.198 r_mcangle_other 2.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.543 r_dihedral_angle_2_deg 9.729 r_long_range_B_refined 6.321 r_long_range_B_other 6.32 r_dihedral_angle_1_deg 5.281 r_scangle_other 3.885 r_scbond_other 2.688 r_scbond_it 2.687 r_mcangle_it 2.198 r_mcangle_other 2.197 r_angle_refined_deg 1.81 r_mcbond_it 1.638 r_mcbond_other 1.513 r_angle_other_deg 0.831 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_4_deg 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 1522 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction