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Crystal structure of ZAD-domain of Serendipity-d protein from D.melanogaster
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 0.1M HEPES pH 7.5, 1.3M Lithium sulfate 1.3M, 0.1M Sodium chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.161 α = 90 b = 99.161 β = 90 c = 117.667 γ = 90
Symmetry Space Group P 43 21 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 2015-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 2.85 99.16 91.3 0.089 0.1 0.045 0.994 9 4.5 12833
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 2.85 3 92.9 0.853 0.961 0.431 0.649 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.85 70.12 12183 633 89.8 0.2187 0.2176 0.2404 0.2278 RANDOM 79.734
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] 0.96 0.96 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.638 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 19.672 r_dihedral_angle_1_deg 11.445 r_angle_refined_deg 2.542 r_angle_other_deg 1.427 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.638 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 19.672 r_dihedral_angle_1_deg 11.445 r_angle_refined_deg 2.542 r_angle_other_deg 1.427 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1376 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling SHELX phasing PDB_EXTRACT data extraction