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Crystal structure of L-rhamnonate dehydratase from Gibberella zeae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 0.1M Tris-HCl, pH 7.0, 2M Ammonium sulfate, 0.2M Lithium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.404 α = 90 b = 201.135 β = 90 c = 82.402 γ = 90
Symmetry Space Group P 21 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 MAR CCD 165 mm MIRRORS 2006-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97960 APS 31-ID
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 2.1 50 95.6 0.085 0.071 5.2 4 187072 187072 30.795
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 92.7 0.36 0.47 1 2.9 17972
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.1 20 181169 181169 5684 95.57 0.19197 0.19197 0.18999 0.1915 0.25589 0.2538 RANDOM 45.657
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] -0.14 -1.03 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.66 r_dihedral_angle_3_deg 18.955 r_dihedral_angle_4_deg 17.702 r_scangle_it 11.616 r_scbond_it 9.403 r_dihedral_angle_1_deg 7.934 r_mcangle_it 7.246 r_mcbond_it 5.819 r_angle_refined_deg 1.16 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.66 r_dihedral_angle_3_deg 18.955 r_dihedral_angle_4_deg 17.702 r_scangle_it 11.616 r_scbond_it 9.403 r_dihedral_angle_1_deg 7.934 r_mcangle_it 7.246 r_mcbond_it 5.819 r_angle_refined_deg 1.16 r_nbtor_refined 0.302 r_xyhbond_nbd_refined 0.164 r_nbd_refined 0.146 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.116 r_chiral_restr 0.103 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 24800 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 180
Software Software Software Name Purpose SHELX model building REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHELX phasing