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LINE-1 endonuclease domain complex with Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 298 0.1M LiSO4; 26% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.857 α = 90 b = 126.776 β = 98.944 c = 44.854 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 180 IMAGE PLATE RIGAKU RAXIS IV++ 2019-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.01 50 98.2 0.089 0.104 0.055 0.998 16.3 3.5 30980 28.32
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 2.01 2.04 93.7 0.75 0.627 1.54 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1VYB 2.01 33.3 1.34 30956 1997 98.21 0.1949 0.192 0.1928 0.2361 0.2368 33.53
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.4637 f_angle_d 1.0992 f_chiral_restr 0.0532 f_bond_d 0.0081 f_plane_restr 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3740 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing