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Crystal structure of NAD binding oxidoreductase from Klebsiella pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 20% (w/v) PEG 3350, 0.2M di-Amonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.418 α = 90 b = 113.026 β = 90.54 c = 132.174 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 225 mm CCD beryllium lens 2012-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.42 50 99.4 0.091 21.7 4.3 65155 65155 -3
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 2.42 2.46 98.9 0.648 2.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.42 50 61607 61607 3272 99.3 0.18805 0.18584 0.22978 0.2112 RANDOM 52.332
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] -2.36 -0.34 6.45 -4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 20.007 r_dihedral_angle_3_deg 15.97 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.641 r_angle_other_deg 1.385 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.495 r_dihedral_angle_4_deg 20.007 r_dihedral_angle_3_deg 15.97 r_dihedral_angle_1_deg 6.01 r_angle_refined_deg 1.641 r_angle_other_deg 1.385 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11513 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 41
Software Software Software Name Purpose HKL-3000 phasing SHELXE model building MLPHARE phasing DM model building ARP/wARP model building REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling DM phasing