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Crystal Structure of Lactococcus lactis Thioredoxin Reductase Exposed to Visible Light (180 min)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 35% PEG 1500, 400 mM Li2SO4, 20 mM HEPES
Crystal Properties Matthews coefficient Solvent content 3.3 62.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.92 α = 90 b = 120.92 β = 90 c = 60.45 γ = 90
Symmetry Space Group P 41 21 2
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 225 mm CCD 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.81 85.51 99.9 0.088 0.999 17.5 10.2 41622
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 1.81 1.84 99.9 1.063 0.317 1.9 8.1
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 1F6M 1.81 54.13 39524 2050 99.85 0.1916 0.1895 0.1994 0.232 0.2396 RANDOM 30.017
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] 0.47 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_4_deg 20.572 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 7.101 r_mcangle_it 4.089 r_mcbond_it 3.111 r_mcbond_other 3.11 r_angle_refined_deg 2.295 r_angle_other_deg 0.951 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.02 r_dihedral_angle_4_deg 20.572 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 7.101 r_mcangle_it 4.089 r_mcbond_it 3.111 r_mcbond_other 3.11 r_angle_refined_deg 2.295 r_angle_other_deg 0.951 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing