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D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with D-allothreonine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 13% PEG3350, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.978 α = 90 b = 157.978 β = 90 c = 158.86 γ = 90
Symmetry Space Group I 41 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 CCD ADSC QUANTUM 270 2012-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.6 50 99.9 0.092 33.65 14.8 130617 130617
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 1.6 1.63 100 0.573 6.89 14.7 6506
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 1.6 26.33 123909 6531 99.75 0.16666 0.16582 0.1634 0.18235 0.1798 RANDOM 22.073
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] -0.37 -0.37 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_4_deg 19.422 r_dihedral_angle_3_deg 13.42 r_dihedral_angle_1_deg 5.974 r_angle_refined_deg 2.591 r_chiral_restr 0.206 r_bond_refined_d 0.029 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_4_deg 19.422 r_dihedral_angle_3_deg 13.42 r_dihedral_angle_1_deg 5.974 r_angle_refined_deg 2.591 r_chiral_restr 0.206 r_bond_refined_d 0.029 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5731 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 49
Software Software Software Name Purpose ADSC data collection SHELXCD phasing SHELXE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling