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Dimerization domain of Xenopus laevis LDB1 in complex with darpin 3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M TrisHCL, pH 7.0
32% PEG200
0.05 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.217 α = 90 b = 70.217 β = 90 c = 122.257 γ = 120
Symmetry Space Group P 32 2 1
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 PILATUS3 S 6M 2017-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.978860 Diamond I24
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 2.05 43.15 99.92 0.127 0.129 0.021 1 23.5 39.5 22528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12
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 SAD THROUGHOUT 2.05 43.15 21557 1071 99.91 0.2206 0.2179 0.231 0.2793 0.284 RANDOM 57.123
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] -0.84 -0.42 -0.84 2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 24.469 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 1.722 r_angle_other_deg 1.304 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 24.469 r_dihedral_angle_3_deg 16.869 r_dihedral_angle_1_deg 6.531 r_angle_refined_deg 1.722 r_angle_other_deg 1.304 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling SHELXCD phasing XDS data reduction