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Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M Bis-Tris HCl, 18% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.04 α = 90 b = 78.776 β = 90 c = 129.686 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 1.3 50 89.4 0.085 147720 147720
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.35 28.3
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 1.3 50 147720 140234 7390 89.25 0.17304 0.17304 0.17201 0.1816 0.19313 0.2034 RANDOM 14.567
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] 0.05 0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_3_deg 12.193 r_sphericity_bonded 7.216 r_dihedral_angle_1_deg 5.944 r_rigid_bond_restr 2.874 r_scangle_it 2.177 r_sphericity_free 1.869 r_scbond_it 1.463 r_angle_refined_deg 1.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_dihedral_angle_4_deg 12.511 r_dihedral_angle_3_deg 12.193 r_sphericity_bonded 7.216 r_dihedral_angle_1_deg 5.944 r_rigid_bond_restr 2.874 r_scangle_it 2.177 r_sphericity_free 1.869 r_scbond_it 1.463 r_angle_refined_deg 1.235 r_mcangle_it 0.901 r_angle_other_deg 0.806 r_mcbond_it 0.784 r_symmetry_vdw_other 0.254 r_nbd_refined 0.203 r_nbd_other 0.188 r_nbtor_refined 0.174 r_mcbond_other 0.158 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.11 r_nbtor_other 0.081 r_chiral_restr 0.074 r_metal_ion_refined 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6038 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement BOS data collection SCALEPACK data scaling