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Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUL apo model of nadD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 bis-tris propane, trisodium citrate, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.16 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.189 α = 90 b = 65.199 β = 90 c = 110.121 γ = 90
Symmetry Space Group P 2 2 21
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 4 mirrors 2004-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.000 Photon Factory BL-18B
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 1.88 50 98.9 0.063 14 7 272399 272302 -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) 1.88 1.95 90.1 0.351 6.6 3488
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo model of nadD 2 15 30716 30716 1594 95 0.1715 0.1644 0.2429 0.2252 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 8 3614
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.105 s_non_zero_chiral_vol 0.042 s_zero_chiral_vol 0.032 s_from_restr_planes 0.0272 s_angle_d 0.024 s_bond_d 0.006 s_anti_bump_dis_restr 0.006 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 75
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling SHELXL refinement