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Crystal structure of L-Rhamnonate dehydratase from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSH PDB entry 2GSH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 60% v/v tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.248 α = 90 b = 272.248 β = 90 c = 272.248 γ = 90
Symmetry Space Group F 4 3 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 MAR CCD 165 mm SGX-CAT 2006-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97900 APS 31-ID
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 1.77 50 99.9 0.086 8.3 21.1 83847
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 1.77 1.83 100 0.678 16.3 8274
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 2GSH 1.8 19.65 74139 3873 0.20351 0.20097 0.2023 0.25235 0.2534 RANDOM 26.298
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 18.084 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 6.551 r_scangle_it 4.468 r_scbond_it 2.935 r_angle_refined_deg 1.788 r_mcangle_it 1.736 r_mcbond_it 1.078 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.576 r_dihedral_angle_4_deg 18.084 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 6.551 r_scangle_it 4.468 r_scbond_it 2.935 r_angle_refined_deg 1.788 r_mcangle_it 1.736 r_mcbond_it 1.078 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.198 r_metal_ion_refined 0.181 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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_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 6273 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SHELX refinement DENZO data reduction PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing