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Crystal structure of mutant CJ YCEI protein (CJ-G34C) with selenocysteine guest structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 3.2 M Ammonium Sulfate, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 5.73 78.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.022 α = 90 b = 178.022 β = 90 c = 50.707 γ = 120
Symmetry Space Group P 6 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 100 CMOS RDI CMOS_8M 2016-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 38.57 99.7 0.204 0.21 0.048 10.7 18.5 10946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 98.3 2.341 2.341 2.441 0.675 0.3 12.5
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 5W2D 2.9 38.57 10365 549 99.24 0.2151 0.2127 0.2191 0.2608 0.2681 RANDOM 97.817
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] 4.46 2.23 4.46 -14.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.047 r_dihedral_angle_3_deg 20.393 r_dihedral_angle_4_deg 19.19 r_dihedral_angle_1_deg 7.787 r_angle_refined_deg 1.693 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1323 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing