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2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone
Crystal Properties Matthews coefficient Solvent content 2.45 49.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 279.621 α = 90 b = 45.585 β = 101.58 c = 112.335 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 lenses 2009-09-13 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 2.14 30 98.2 0.084 27 6.6 75710 75710 -3 34.7
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 2.14 2.18 93.5 0.491 3.5 6 3610
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 (All) 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 2.14 29.93 71864 71864 3806 98 0.21387 0.21387 0.21092 0.2192 0.26879 0.2754 RANDOM 27.209
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] -1.57 0.23 5.13 -3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.664 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_4_deg 10.682 r_scangle_it 4.87 r_scbond_it 3.469 r_dihedral_angle_1_deg 2.762 r_mcangle_it 2.147 r_angle_refined_deg 1.453 r_mcbond_it 1.286 r_angle_other_deg 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.664 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_4_deg 10.682 r_scangle_it 4.87 r_scbond_it 3.469 r_dihedral_angle_1_deg 2.762 r_mcangle_it 2.147 r_angle_refined_deg 1.453 r_mcbond_it 1.286 r_angle_other_deg 0.87 r_mcbond_other 0.375 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9900 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 243
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing