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2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: Classics II (B11), 2.1M DL-Malic acid (pH 7.0);
Cryo: Screen : 50% Sucrose (1:1).
Crystal Properties Matthews coefficient Solvent content 3.27 62.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.884 α = 90 b = 137.884 β = 90 c = 204.281 γ = 90
Symmetry Space Group P 41 21 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 MARMOSAIC 225 mm CCD C(111) 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.75 30 100 0.135 0.135 17.8 7.9 51774 -3 53.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 100 0.736 0.849 3.1 8 2554
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 SAD THROUGHOUT 2.75 29.81 49001 2618 99.61 0.18656 0.1848 0.1979 0.21996 0.2295 RANDOM 46.485
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] -2.19 -2.19 4.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.26 r_dihedral_angle_3_deg 10.066 r_dihedral_angle_4_deg 9.524 r_long_range_B_refined 4.642 r_long_range_B_other 4.576 r_dihedral_angle_1_deg 2.354 r_scangle_other 1.849 r_angle_refined_deg 1.673 r_mcangle_it 1.348 r_mcangle_other 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.26 r_dihedral_angle_3_deg 10.066 r_dihedral_angle_4_deg 9.524 r_long_range_B_refined 4.642 r_long_range_B_other 4.576 r_dihedral_angle_1_deg 2.354 r_scangle_other 1.849 r_angle_refined_deg 1.673 r_mcangle_it 1.348 r_mcangle_other 1.348 r_scbond_it 1.327 r_scbond_other 1.327 r_angle_other_deg 0.905 r_mcbond_it 0.769 r_mcbond_other 0.769 r_chiral_restr 0.095 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.008 r_bond_other_d 0.002 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 10227 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing