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X-ray crystal structure of a nicotinate nucleotide adenylyltransferase from Burkholderia thailandensis bound to NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 289 JCSG+ C1: 0.1 M sodium phosphate pH 4.2, 0.2 M sodium chloride, 20% PEG 8000; ButhA.00448.a.A1.PS01231 at 20 mg/ml
Crystal Properties Matthews coefficient Solvent content 3.17 61.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.2 α = 90 b = 91.32 β = 116.88 c = 60.13 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 ADSC QUANTUM 315r 2012-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.05 50 97 0.098 0.117 10.45 3.19 37482 -3 19.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 99.1 0.477 0.572 2.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 1K4M 2.05 37.963 1.36 37462 1905 97.28 0.2032 0.2013 0.2046 0.2383 0.2401 RANDOM 24.649
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 f_dihedral_angle_d 13.736 f_angle_d 0.678 f_chiral_restr 0.027 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3429 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 98
Software Software Software Name Purpose XDS data reduction PHENIX refinement XSCALE data scaling BALBES phasing PDB_EXTRACT data extraction