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Crystal structure of lambda exonuclease in complex with the Red beta C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 PEG3350, LISO4, BIS-TRIS
Crystal Properties Matthews coefficient Solvent content 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.522 α = 90 b = 122.522 β = 90 c = 147.858 γ = 120
Symmetry Space Group P 31 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 R 200K-A mirrors 2018-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-003 1.54
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 2.3 106.11 99.7 0.13 0.149 0.071 6.8 3.9 57486
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 2.3 2.34 99.1 0.58 0.747 0.46 0.461 2.3
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 1AVQ 2.3 106.11 54662 2782 99.65 0.1982 0.1953 0.1996 0.2535 0.2542 RANDOM 31.808
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] 0.14 0.07 0.14 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_1_deg 5.804 r_angle_refined_deg 1.271 r_angle_other_deg 0.938 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 16.134 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_1_deg 5.804 r_angle_refined_deg 1.271 r_angle_other_deg 0.938 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6890 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 80
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing