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Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate
Crystallization Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.52 α = 90 b = 105.52 β = 90 c = 160.077 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 88.04 20245
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 2.9 50 18872 981 95.8 0.23373 0.23132 0.2302 0.28031 0.2806 RANDOM 22.971
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] -0.69 -0.69 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.207 r_dihedral_angle_4_deg 20.907 r_dihedral_angle_3_deg 20.007 r_dihedral_angle_1_deg 7.306 r_scangle_it 1.873 r_angle_refined_deg 1.579 r_scbond_it 1.16 r_mcangle_it 0.951 r_mcbond_it 0.523 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.207 r_dihedral_angle_4_deg 20.907 r_dihedral_angle_3_deg 20.007 r_dihedral_angle_1_deg 7.306 r_scangle_it 1.873 r_angle_refined_deg 1.579 r_scbond_it 1.16 r_mcangle_it 0.951 r_mcbond_it 0.523 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.224 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5469 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement