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Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DZR PDB ENTRY 1DZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15% PEG 3350, 0.1M Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.147 α = 90 b = 73.145 β = 90 c = 126.242 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 MONOCHROMETER 2004-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.89 50 99.9 0.06 15.5 6.6 35811 35811 -3 24.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.89 1.96 99.7 0.379 6.43 6.3 3486
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 1DZR 1.9 20 33411 1759 99.98 0.19957 0.19705 0.2074 0.2463 0.2526 RANDOM 26.019
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] 0.87 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.914 r_scangle_it 5.327 r_scbond_it 3.488 r_mcangle_it 2.312 r_angle_refined_deg 2.137 r_mcbond_it 1.392 r_angle_other_deg 1.011 r_symmetry_hbond_refined 0.31 r_symmetry_vdw_other 0.297 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.914 r_scangle_it 5.327 r_scbond_it 3.488 r_mcangle_it 2.312 r_angle_refined_deg 2.137 r_mcbond_it 1.392 r_angle_other_deg 1.011 r_symmetry_hbond_refined 0.31 r_symmetry_vdw_other 0.297 r_nbd_other 0.26 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.147 r_nbtor_other 0.094 r_bond_refined_d 0.03 r_gen_planes_other 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2915 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALEPACK data scaling MOLREP phasing