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Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (NP_809094.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.54 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.09 41.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.215 α = 90 b = 42.215 β = 90 c = 186.713 γ = 90
Symmetry Space Group P 43 21 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 Flat mirror, vertical and horizontal focussing mirrors 2009-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
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 1.54 29.854 98.6 0.11 0.11 11 6.2 25905
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 1.54 1.58 87.5 0.55 0.55 1.4 3.1 1631
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 SAD THROUGHOUT 1.54 29.854 25811 1313 98.59 0.147 0.146 0.1599 0.176 0.1921 RANDOM 12.866
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.2 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 12.52 r_scangle_it 6.297 r_dihedral_angle_1_deg 5.713 r_scbond_it 4.223 r_mcangle_it 2.379 r_angle_refined_deg 1.564 r_mcbond_it 1.454 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.2 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 12.52 r_scangle_it 6.297 r_dihedral_angle_1_deg 5.713 r_scbond_it 4.223 r_mcangle_it 2.379 r_angle_refined_deg 1.564 r_mcbond_it 1.454 r_angle_other_deg 0.919 r_mcbond_other 0.439 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1333 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing