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Crystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 1.5 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 0.1 M BisTrispropane (pH 7.5), 0.2 M potassium thiocyanate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.487 α = 90 b = 64.786 β = 102.33 c = 69.118 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 90 CCD RAYONIX MX300HE 2014-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 50 98.8 0.037 0.037 0.04 0.014 21.9 6.2 61319
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 1.5 1.53 97.7 0.446 0.497 0.219 0.922 2.724 5 3013
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 4WNE 1.5 46.79 58188 3108 98.32 0.1636 0.1626 0.1714 0.1824 0.1926 RANDOM 24.126
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] 0.42 -0.45 0.97 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.874 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_1_deg 4.727 r_angle_refined_deg 1.105 r_angle_other_deg 0.698 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.874 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 13.749 r_dihedral_angle_1_deg 4.727 r_angle_refined_deg 1.105 r_angle_other_deg 0.698 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2767 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 90
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction