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A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HCS PDB entry 3HCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 273 0.1 M HEPES, 10% PEG 8K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.67 α = 90 b = 52.32 β = 90 c = 73.97 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 PIXEL PSI PILATUS 6M 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 ALBA XALOC
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 1.55 50 94 0.055 10.2 2.9 28019 -3 30.4
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 1.55 1.59 94.7 0.799 1.3 2.85
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 3HCS 1.55 42.71 26618 1401 94 0.2113 0.20983 0.2162 0.2392 0.2439 RANDOM 28.216
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] 0.26 0.34 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.767 r_dihedral_angle_4_deg 20.357 r_dihedral_angle_3_deg 14.09 r_long_range_B_refined 7.786 r_long_range_B_other 7.687 r_dihedral_angle_1_deg 6.04 r_scangle_other 3.684 r_scbond_it 2.939 r_scbond_other 2.938 r_mcangle_other 2.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.767 r_dihedral_angle_4_deg 20.357 r_dihedral_angle_3_deg 14.09 r_long_range_B_refined 7.786 r_long_range_B_other 7.687 r_dihedral_angle_1_deg 6.04 r_scangle_other 3.684 r_scbond_it 2.939 r_scbond_other 2.938 r_mcangle_other 2.493 r_mcangle_it 2.492 r_angle_refined_deg 2.142 r_mcbond_it 1.654 r_mcbond_other 1.649 r_angle_other_deg 1.057 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 1512 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing