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Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 0.2M MgCl2, 20.0% PEG 1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.331 α = 90 b = 145.684 β = 91.92 c = 100.208 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 325 mm CCD Flat mirror (vertical focusing) 2007-12-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97941, 0.97883 SSRL BL11-1
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 2.4 29.45 99 0.133 0.133 9.3 3.6 52411 33.924
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 2.4 2.46 91.8 0.429 0.429 1.9 2 3467
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.4 29.45 52383 2662 99.02 0.196 0.193 0.1965 0.243 0.2442 RANDOM 45.891
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] 4.46 -0.01 -2.35 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_4_deg 12.6 r_dihedral_angle_1_deg 4.653 r_scangle_it 1.987 r_scbond_it 1.317 r_angle_refined_deg 0.934 r_mcangle_it 0.752 r_mcbond_it 0.409 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.841 r_dihedral_angle_3_deg 13.561 r_dihedral_angle_4_deg 12.6 r_dihedral_angle_1_deg 4.653 r_scangle_it 1.987 r_scbond_it 1.317 r_angle_refined_deg 0.934 r_mcangle_it 0.752 r_mcbond_it 0.409 r_nbtor_refined 0.292 r_nbd_refined 0.168 r_xyhbond_nbd_refined 0.101 r_symmetry_vdw_refined 0.1 r_chiral_restr 0.057 r_symmetry_hbond_refined 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10435 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing SHARP phasing