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Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D2X PDB enrty 2D2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 277 40%(w/v) PEG 4000, 200mM Li2SO4, 100mM Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.569 α = 90 b = 70.108 β = 117.61 c = 81.569 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 210 2006-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.15 72.36 99.2 43452 43452
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.23 97.5
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 PDB enrty 2D2X 2.15 40.72 40936 40936 2170 99.23 0.17599 0.17599 0.17352 0.1727 0.22257 0.2209 RANDOM 25.807
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] -0.15 0.23 1.07 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.603 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 17.251 r_dihedral_angle_1_deg 6.062 r_scangle_it 4.474 r_scbond_it 3.07 r_mcangle_it 1.937 r_angle_refined_deg 1.927 r_mcbond_it 1.168 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.603 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_3_deg 17.251 r_dihedral_angle_1_deg 6.062 r_scangle_it 4.474 r_scbond_it 3.07 r_mcangle_it 1.937 r_angle_refined_deg 1.927 r_mcbond_it 1.168 r_nbtor_refined 0.313 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.234 r_symmetry_vdw_refined 0.206 r_chiral_restr 0.17 r_xyhbond_nbd_refined 0.169 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 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 5717 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling XFIT data reduction