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Crystal structure of an esterase from Aspergillus oryzae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 ammonium sulphate, Tris buffer 2 VAPOR DIFFUSION, SITTING DROP 293 lithium sulphate, tris buffer,CRYSTALS SOAKED IN 5mM KPTCL4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.472 α = 90 b = 119.472 β = 90 c = 142.85 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-F 2012-05-28 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2012-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1 2 SYNCHROTRON DIAMOND BEAMLINE I04 1.072 Diamond I04
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 2.1 37.72 100 0.099 25.6 18.5 67326 24.8
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 2.1 2.15 100 0.74 0.78 0.25 0.93 4.8 19.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.1 37.72 64050 3246 99.98 0.15584 0.15385 0.19429 0.1841 RANDOM 30.347
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] 0.26 0.13 0.26 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.368 r_dihedral_angle_4_deg 23.671 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 5.287 r_long_range_B_other 5.263 r_scangle_other 4.323 r_mcangle_it 3.083 r_mcangle_other 3.083 r_scbond_it 3.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.368 r_dihedral_angle_4_deg 23.671 r_dihedral_angle_3_deg 14.281 r_dihedral_angle_1_deg 6.695 r_long_range_B_refined 5.287 r_long_range_B_other 5.263 r_scangle_other 4.323 r_mcangle_it 3.083 r_mcangle_other 3.083 r_scbond_it 3.014 r_scbond_other 2.982 r_mcbond_it 2.329 r_mcbond_other 2.329 r_angle_refined_deg 1.743 r_angle_other_deg 0.916 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7777 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK phasing