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Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 293 2.0M Na/K pH 7.1, 34% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.788 α = 90 b = 229.495 β = 96.95 c = 74.583 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU JUPITER 2005-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 2.07 50 5 150049
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.14 99.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1DZR 2.07 20 149849 134914 14935 99.5 0.225 0.20854 0.20313 0.2076 0.2571 0.1994 RANDOM 31.442
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] 1.37 -0.6 -1.09 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 7.112 r_scangle_it 2.896 r_scbond_it 1.972 r_angle_refined_deg 1.381 r_mcangle_it 1.203 r_mcbond_it 1.015 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.853 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 7.112 r_scangle_it 2.896 r_scbond_it 1.972 r_angle_refined_deg 1.381 r_mcangle_it 1.203 r_mcbond_it 1.015 r_nbtor_refined 0.312 r_xyhbond_nbd_refined 0.294 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_chiral_restr 0.095 r_bond_refined_d 0.012 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 17364 Nucleic Acid Atoms Solvent Atoms 1747 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing