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Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 277 NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.54 α = 90 b = 36.32 β = 125.46 c = 72.6 γ = 90
Symmetry Space Group C 1 2 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) 2008-02-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97922, 0.97874 SSRL BL11-1
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 1.5 25.872 98.3 0.038 11.53 30979 -3 17.062
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 1.5 1.55 96.7 0.362 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.5 25.872 30979 1560 99.56 0.182 0.18 0.217 0.2195 RANDOM 15.356
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] -0.75 -1 0.29 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.877 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_3_deg 11.479 r_scangle_it 6.33 r_scbond_it 4.39 r_dihedral_angle_1_deg 3.972 r_mcangle_it 2.848 r_mcbond_it 1.826 r_angle_refined_deg 1.563 r_angle_other_deg 1.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.877 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_3_deg 11.479 r_scangle_it 6.33 r_scbond_it 4.39 r_dihedral_angle_1_deg 3.972 r_mcangle_it 2.848 r_mcbond_it 1.826 r_angle_refined_deg 1.563 r_angle_other_deg 1.065 r_mcbond_other 0.527 r_chiral_restr 0.078 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1472 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing