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Crystal structure of beta secetase in complex with 2-amino-3-methyl-6-((1S,2R)-2-(3'-methylbiphenyl-4-yl)cyclopropyl)pyrimidin-4(3H)-one
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 120mM sodium citrate, 200mM ammonium iodide, 30%(w/v) polyethylene glycol 5000 monomethyl ether, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.92 α = 90 b = 101.92 β = 90 c = 169.26 γ = 120
Symmetry Space Group P 61 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 88.265 94.8 0.118 8.1 4.1 17437 17437
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 2.5 2.64 93.7 0.466 0.466 0.572 0.244 1.6 5.2 2452
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 20 17419 892 93.64 0.2272 0.2241 0.2267 0.2866 0.2857 RANDOM 37.8301
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_4_deg 22.399 r_dihedral_angle_3_deg 17.121 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.219 r_scbond_it 1.989 r_mcangle_it 1.559 r_angle_refined_deg 1.381 r_mcbond_it 0.845 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.536 r_dihedral_angle_4_deg 22.399 r_dihedral_angle_3_deg 17.121 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.219 r_scbond_it 1.989 r_mcangle_it 1.559 r_angle_refined_deg 1.381 r_mcbond_it 0.845 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2790 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 31
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction