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Crystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and Sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other inhouse
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 0.1M amino acid stock (0.2M L-Na-Glutamate; 0.2M Alananine (racemic); 0.2M Glycine; 0.2M Lysine HCL (racemic); 0.2M Serine (racemic), 0.1M Imidazole; MES monohydrate (acid) pH 6.5, 50% v/v precipitant mix (25% v/v MPD; 25% PEG 1000; 25% PEG 3350) Morpheus condition H4
Crystal Properties Matthews coefficient Solvent content 2.01 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.961 α = 90 b = 75.797 β = 94.62 c = 64.345 γ = 90
Symmetry Space Group P 1 21 1
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 S 6M 2016-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.45 37.02 99.38 0.049 0.058 0.031 1 15.5 3.3 72308 12.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.502 99.71 0.25 0.31 0.17 0.98 5.32 3
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 inhouse 1.45 37.02 1.38 72301 3514 99.38 0.1202 0.1188 0.1195 0.146 0.1482
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 2.797 f_angle_d 1.114 f_chiral_restr 0.09 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3381 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing