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Structure of EED bound to EEDi-4259
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2uL of protein + 2 uL of well (0.1 M Tris pH 8.5, 20% glycerol, 4.3 M Na Formate, 10 mM TCEP)
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.867 α = 90 b = 85.024 β = 90 c = 91.988 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 CCD MARMOSAIC 300 mm CCD 2018-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 100 0.093 0.101 0.037 7.3 7.3 36678 21.61
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 1.9 1.93 100 0.661 0.711 0.262 0.855 7.3
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 in house structure 1.9 18 36515 1799 99.7 0.162 0.16 0.1558 0.19 0.1876 RANDOM 23.28
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] 0.9715 0.1026 -1.0742
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.2 t_other_torsion 2.79 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.2 t_other_torsion 2.79 t_angle_deg 1.03 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2867 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling BUSTER refinement PDB_EXTRACT data extraction MOLREP phasing