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Crystal structure of ZAD-domain of ZNF_276 protein from rabbit.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M bicine pH 8.5, PEG 20000 5%, dextrane sulfate 5%
Crystal Properties Matthews coefficient Solvent content 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.94 α = 90 b = 82.94 β = 90 c = 134.32 γ = 120
Symmetry Space Group P 63 2 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 PIXEL DECTRIS PILATUS 6M 2021-06-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313, 1.282 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.9 49.1 98.8 0.052 0.054 0.999 25.91 11.043 6460 108.322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.8 1.363 1.42 0.744 1.87 11.586
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.9 49.1 6459 609 98.777 0.295 0.2896 0.2891 0.3399 0.3409 RANDOM 99.154
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] 0.526 0.263 0.526 -1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_3_deg 23.432 r_dihedral_angle_4_deg 17.116 r_lrange_it 13.492 r_lrange_other 13.481 r_scangle_it 11.897 r_scangle_other 11.89 r_mcangle_it 11.596 r_mcangle_other 11.588 r_dihedral_angle_1_deg 10.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.911 r_dihedral_angle_3_deg 23.432 r_dihedral_angle_4_deg 17.116 r_lrange_it 13.492 r_lrange_other 13.481 r_scangle_it 11.897 r_scangle_other 11.89 r_mcangle_it 11.596 r_mcangle_other 11.588 r_dihedral_angle_1_deg 10.503 r_scbond_it 9.42 r_scbond_other 9.413 r_mcbond_other 7.766 r_mcbond_it 7.761 r_angle_refined_deg 2.922 r_angle_other_deg 1.467 r_xyhbond_nbd_refined 0.209 r_ncsr_local_group_1 0.202 r_nbd_other 0.165 r_nbd_refined 0.161 r_nbtor_refined 0.137 r_chiral_restr 0.123 r_symmetry_nbd_other 0.12 r_symmetry_nbtor_other 0.074 r_symmetry_nbd_refined 0.074 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 977 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXDE phasing PDB_EXTRACT data extraction