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Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in complex with adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2M Sodium acetate, 0.1M Tris pH 8.5, 30% PEG 4000, soaked with 5mM adenine
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.015 α = 90 b = 75.207 β = 90 c = 171.999 γ = 90
Symmetry Space Group P 21 21 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 315r 2014-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 44.4 99.7 0.121 0.13 0.045 6.9 8.4 56827
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99 0.795 0.852 0.302 0.814 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5YW2 1.9 44.4 53991 2774 99.61 0.1829 0.1804 0.1907 0.2321 0.2386 RANDOM 28.213
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] -1.58 1.79 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 16.387 r_dihedral_angle_1_deg 6.918 r_angle_refined_deg 2.367 r_angle_other_deg 1.164 r_chiral_restr 0.142 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.471 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 16.387 r_dihedral_angle_1_deg 6.918 r_angle_refined_deg 2.367 r_angle_other_deg 1.164 r_chiral_restr 0.142 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5253 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 40
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing