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2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 297 Protein: 7.5 mg/mL in buffer containing 10 mM Tris HCl pH 8.3, 500 mM NaCl, and 5 mM BME, 5 mM MgCl2, 1 mM NADP+, and 10% glycerol.Crystallization conditions: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, and 25% w/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 3.32 62.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.449 α = 90 b = 113.337 β = 91.18 c = 144.949 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 MARMOSAIC 300 mm CCD Mirror 2011-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97856 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.65 30 100 0.102 11.49 3.8 75200 75200 -3 67.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 100 0.615 2.35 3.8 3724
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 (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 1VL0 2.65 29.9 70861 70861 3745 99.94 0.21747 0.21531 0.2194 0.25785 0.2619 RANDOM 56.691
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] 4.94 0.53 -0.35 -4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.937 r_dihedral_angle_4_deg 4.542 r_dihedral_angle_3_deg 4.01 r_scangle_it 3.011 r_scbond_it 1.822 r_angle_refined_deg 1.359 r_mcangle_it 1.172 r_angle_other_deg 0.791 r_dihedral_angle_1_deg 0.68 r_mcbond_it 0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 9.937 r_dihedral_angle_4_deg 4.542 r_dihedral_angle_3_deg 4.01 r_scangle_it 3.011 r_scbond_it 1.822 r_angle_refined_deg 1.359 r_mcangle_it 1.172 r_angle_other_deg 0.791 r_dihedral_angle_1_deg 0.68 r_mcbond_it 0.606 r_mcbond_other 0.103 r_chiral_restr 0.083 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13571 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 373
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling