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Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from Parabacteroides distasonis ATCC 8503 at 1.86 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.47 293 14.0000% polyethylene glycol 1000, 0.3000M sodium chloride, 0.1M Na/K phosphate pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.49 64.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.639 α = 90 b = 149.639 β = 90 c = 149.639 γ = 90
Symmetry Space Group P 43 3 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 collimating mirror, toroid focusing mirror 2009-11-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97946,0.97932 SSRL BL9-2
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 1.86 29.347 99.8 0.086 12.7 10.669 48462 -3 25.884
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) 1.86 1.93 99.7 0.821 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 1.86 29.347 48417 2446 99.85 0.161 0.16 0.178 0.1739 RANDOM 26.696
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.795 r_dihedral_angle_4_deg 14.534 r_dihedral_angle_3_deg 13.843 r_dihedral_angle_1_deg 5.292 r_scangle_it 4.653 r_scbond_it 3.383 r_mcangle_it 2.507 r_mcbond_it 1.951 r_angle_refined_deg 1.434 r_angle_other_deg 0.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.795 r_dihedral_angle_4_deg 14.534 r_dihedral_angle_3_deg 13.843 r_dihedral_angle_1_deg 5.292 r_scangle_it 4.653 r_scbond_it 3.383 r_mcangle_it 2.507 r_mcbond_it 1.951 r_angle_refined_deg 1.434 r_angle_other_deg 0.988 r_mcbond_other 0.563 r_symmetry_vdw_other 0.286 r_nbd_refined 0.224 r_nbd_other 0.206 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.087 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2676 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing