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Crystal structure of a putative zinc-binding dehydrogenase (gutB) from Clostridium scindens ATCC 35704 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.75 293 0.2M magnesium chloride, 24.0% polyethylene glycol 400, 0.1M HEPES pH 6.75, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.87 α = 90 b = 85.597 β = 90 c = 149.087 γ = 90
Symmetry Space Group I 2 2 2
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 Vertical focusing mirror; double crystal Si(111) monochromator 2013-12-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97939,0.96109,0.97919 SSRL BL14-1
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 29.355 97.8 0.05 10.15 27920 -3 35.548
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 2.07 92.5 0.609 1.4
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 29.355 27918 1403 99.48 0.1705 0.1682 0.1793 0.2159 0.2191 RANDOM 49.1123
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] -2.1 4.29 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.588 r_dihedral_angle_4_deg 17.122 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.394 r_mcangle_it 4.009 r_mcbond_other 2.736 r_mcbond_it 2.735 r_angle_refined_deg 1.779 r_angle_other_deg 0.824 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.588 r_dihedral_angle_4_deg 17.122 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.394 r_mcangle_it 4.009 r_mcbond_other 2.736 r_mcbond_it 2.735 r_angle_refined_deg 1.779 r_angle_other_deg 0.824 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 21
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing