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Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with AMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M Bis-Tris HCl, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.99 38.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.578 α = 90 b = 78.45 β = 90 c = 129.49 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 315 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537 ALS 8.2.2
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 50 91.3 0.142 41903 41903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 60.3
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 FOURIER SYNTHESIS THROUGHOUT 2 46.88 41903 39774 2128 91.3 0.23606 0.23606 0.23249 0.2401 0.3026 0.3078 RANDOM 28.653
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] -0.13 0.32 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.449 r_dihedral_angle_3_deg 14.003 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 6.673 r_scangle_it 1.617 r_angle_refined_deg 1.356 r_scbond_it 1.13 r_angle_other_deg 0.833 r_mcangle_it 0.69 r_mcbond_it 0.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.449 r_dihedral_angle_3_deg 14.003 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_1_deg 6.673 r_scangle_it 1.617 r_angle_refined_deg 1.356 r_scbond_it 1.13 r_angle_other_deg 0.833 r_mcangle_it 0.69 r_mcbond_it 0.557 r_symmetry_vdw_other 0.254 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.211 r_symmetry_hbond_refined 0.21 r_nbd_other 0.194 r_nbtor_refined 0.175 r_mcbond_other 0.132 r_metal_ion_refined 0.108 r_nbtor_other 0.083 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5882 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement BOS data collection SCALEPACK data scaling