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XenA - oxidized - Y183F variant in complex with 7-hydroxycoumarin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 1.4 M ammonium sulfate, 0.1 M HEPES/NaOH pH7.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.76 α = 90 b = 83.41 β = 90 c = 156.91 γ = 90
Symmetry Space Group I 2 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 CCD RAYONIX MX-225 2011-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9180 BESSY 14.2
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 1.13 35 96.9 0.058 13.64 4.2 135813 -3
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 1.13 1.16 90.4 0.423 3.08
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 3L5L 1.133 29.372 1.99 135806 2000 96.87 0.1185 0.1182 0.1163 0.1405 0.1371 13.4
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 12.59 f_angle_d 1.395 f_chiral_restr 0.077 f_bond_d 0.01 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2777 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 119
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction