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Crystal Structure Analysis of 1,5-anhydro-D-fructose reductase from Sinorhizobium meliloti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GLX PDB ENTRY 2GLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 100 mM BisTRIS, 50 mM ammonium sulphate, 20 % (w/v) PEG-3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.895 α = 90 b = 89.672 β = 90 c = 94.487 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Incoatec mirror 2008-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
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 1.93 19.5 99.2 0.1 0.1 26.85 14.3 22202 22202 24.574
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 1.93 1.98 91.5 0.58 0.58 4.66 12.6 1487
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 ENTRY 2GLX 1.93 19.48 22202 21091 1111 99.73 0.16061 0.16061 0.15801 0.1653 0.20971 0.2108 RANDOM 22.894
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] 0.94 -1.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.3 r_dihedral_angle_4_deg 25.17 r_dihedral_angle_3_deg 17.505 r_dihedral_angle_1_deg 7.146 r_angle_refined_deg 1.889 r_angle_other_deg 0.963 r_chiral_restr 0.134 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.3 r_dihedral_angle_4_deg 25.17 r_dihedral_angle_3_deg 17.505 r_dihedral_angle_1_deg 7.146 r_angle_refined_deg 1.889 r_angle_other_deg 0.963 r_chiral_restr 0.134 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2449 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 48
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling