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Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 294 1M potassium/sodium phosphate pH 6.9, 1.25mM DNTB, 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.34 63.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.524 α = 90 b = 73.524 β = 90 c = 130.246 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2009-04-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97953, 0.97940 APS 19-ID
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 2.3 50 99.5 0.082 8.9 11.6 16455 16455 -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 2.3 2.34 100 0.645 10.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 36.76 15584 15584 831 99.44 0.21652 0.21481 0.2156 0.25075 0.2434 RANDOM 56.042
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] 2.63 2.63 -5.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_1_deg 7.182 r_scangle_it 4.469 r_scbond_it 2.702 r_angle_refined_deg 1.621 r_mcangle_it 1.544 r_angle_other_deg 0.884 r_mcbond_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 14.586 r_dihedral_angle_1_deg 7.182 r_scangle_it 4.469 r_scbond_it 2.702 r_angle_refined_deg 1.621 r_mcangle_it 1.544 r_angle_other_deg 0.884 r_mcbond_it 0.814 r_mcbond_other 0.189 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1508 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 13
Software Software Software Name Purpose SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building