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Crystal structure of mutant CJ YCEI protein (CJ-G34C) with 5-mercapto-2-nitrobenzoic acid 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 5.7 78.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.337 α = 90 b = 178.337 β = 90 c = 50.318 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 2016-04-06 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 38.114 99.7 0.255 0.262 0.059 9.4 20.1 10917
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 99.1 4.122 4.122 4.23 0.945 0.2 20
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 38.114 10351 547 99.52 0.2187 0.2158 0.2196 0.2732 0.2777 RANDOM 99.483
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] 4.1 2.05 4.1 -13.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_3_deg 20.878 r_dihedral_angle_4_deg 18.072 r_dihedral_angle_1_deg 7.789 r_angle_refined_deg 1.688 r_chiral_restr 0.109 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1323 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 40
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing