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Crystal structure of the oxidized TPR domain of LGN in complex with Frmpd4/Preso1 at 2.9 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 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M BisTrispropane (pH 7.5), 0.2 M potassium thiocyanate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.599 α = 90 b = 92.599 β = 90 c = 175.238 γ = 120
Symmetry Space Group P 61 2 2
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 2013-12-12 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) 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 2.9 50 99.3 0.075 15 7.2 10385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 100 0.502 2.728 7.6 496
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 2.9 39.12 9777 513 98.71 0.2391 0.237 0.2384 0.2802 0.2803 RANDOM 88.325
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] 3.13 3.13 3.13 -10.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_3_deg 19.496 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_1_deg 5.522 r_angle_refined_deg 1.138 r_angle_other_deg 0.685 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_3_deg 19.496 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_1_deg 5.522 r_angle_refined_deg 1.138 r_angle_other_deg 0.685 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction