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Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6.5 277 0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.478 α = 117.34 b = 74.601 β = 100.95 c = 74.591 γ = 100.71
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 APS sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2004-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 43.34 97.72 0.106 12.88 3.77 54061 30.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 93.79 0.522 2.58 3.43 5179
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 1a9o 2.01 43.34 51297 2755 97.23 0.20575 0.20391 0.2161 0.23995 0.2523 RANDOM 32.66
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] 1.11 1.25 1.4 0.05 0.75 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.602 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_4_deg 12.745 r_scangle_it 7.09 r_dihedral_angle_1_deg 6.321 r_scbond_it 5.208 r_mcangle_it 2.875 r_mcbond_it 2.066 r_angle_refined_deg 1.615 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.602 r_dihedral_angle_3_deg 14.531 r_dihedral_angle_4_deg 12.745 r_scangle_it 7.09 r_dihedral_angle_1_deg 6.321 r_scbond_it 5.208 r_mcangle_it 2.875 r_mcbond_it 2.066 r_angle_refined_deg 1.615 r_angle_other_deg 0.964 r_mcbond_other 0.4 r_symmetry_vdw_other 0.333 r_symmetry_hbond_refined 0.248 r_nbd_refined 0.21 r_nbd_other 0.199 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.176 r_symmetry_vdw_refined 0.136 r_chiral_restr 0.096 r_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5591 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement