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Crystal structure of Y200L mutant of Rat Catechol-O-Methyltransferase in complex with AdoMet and 3,5-dinitrocatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 200nl of protein mixed with an equal volume of 0.09 M [0.3 M sodium fluoride; 0.3 M sodium bromide; 0.3 M sodium iodide], 0.1 M Tris / Bicine pH 8.5, 50% [40% v/v PEG 500* MME; 20 % w/v PEG 20000] Morpheus HT96 condition B9
Crystal Properties Matthews coefficient Solvent content 2.8 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.7 α = 90 b = 79.37 β = 90 c = 109.66 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.63 48.713 98 0.139 10.63 7.5 66577
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 1.63 1.68 98 0.756 2.98 7.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NWE 1.63 48.713 1.35 66571 3377 98.06 0.1599 0.1589 0.1599 0.1782 0.1784 Random selection
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 13.314 f_angle_d 1.337 f_chiral_restr 0.079 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3350 Nucleic Acid Atoms Solvent Atoms 729 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing