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Crystal structure of TYR from Ralstonia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.015M Magnesium acetate tetrahydrate,0.05M Sodium cacodylate trihydrate,pH 6.0,1.7M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.31 71.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.897 α = 90 b = 190.897 β = 90 c = 402.109 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9792 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.64 152.9 99.9842 0.138 0.142 0.045 0.999 82467 19.4 1386447 68.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 1.343 0.313 0.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X3P 2.64 48.09 0.31 82437 4105 99.97 0.1824 0.1814 0.187 0.2017 0.2069 67.59
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.3957 f_angle_d 0.6215 f_chiral_restr 0.0448 f_plane_restr 0.0063 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9935 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 15
Software Software Software Name Purpose HKL-3000 data collection PHENIX refinement DIALS data reduction HKL-3000 data scaling PHENIX phasing