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Crystal structure of the human ZRANB3 HNH domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other obtained by SeMet SAD phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% (w/v) PEG10,000 + 100 mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.17 61.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.841 α = 90 b = 67.552 β = 90 c = 92.161 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 DECTRIS PILATUS 2M 2015-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9174 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 54.88 99.9 0.208 0.997 11 13.2 24666
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.7 1.862 0.522 1.4 11.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT obtained by SeMet SAD phasing 2 54.48 23410 1209 99.89 0.194 0.19185 0.23613 0.2205 RANDOM 31.134
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] 0.1 0.31 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.65 r_dihedral_angle_4_deg 20.606 r_dihedral_angle_3_deg 15.743 r_long_range_B_refined 7.578 r_long_range_B_other 7.473 r_dihedral_angle_1_deg 6.647 r_scangle_other 4.772 r_scbond_it 3.124 r_scbond_other 3.122 r_mcangle_other 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.65 r_dihedral_angle_4_deg 20.606 r_dihedral_angle_3_deg 15.743 r_long_range_B_refined 7.578 r_long_range_B_other 7.473 r_dihedral_angle_1_deg 6.647 r_scangle_other 4.772 r_scbond_it 3.124 r_scbond_other 3.122 r_mcangle_other 3.001 r_mcangle_it 2.997 r_mcbond_it 2.069 r_mcbond_other 2.062 r_angle_refined_deg 1.498 r_angle_other_deg 1.017 r_chiral_restr 0.106 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_gen_planes_other 0.008 r_bond_other_d 0.004 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 1904 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing