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Crystal structure of Trichomonas vaginalis purine nucleoside phosphorylase complexed with formycin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 PEG400, ethylene glycol, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.3 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.8 α = 90 b = 136.8 β = 90 c = 136.8 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM 0.9795 APS 8-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 37.94 92.8 13966 13004 27.7
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 2.6 2.76 87.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1PKE 2.6 37.94 13966 13004 636 92.8 0.213 0.213 0.213 0.2086 0.253 0.2411 RANDOM 49.3
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 c_dihedral_angle_d 23 c_scangle_it 3.04 c_scbond_it 2.15 c_mcangle_it 1.95 c_angle_deg 1.3 c_mcbond_it 1.18 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.04 c_scbond_it 2.15 c_mcangle_it 1.95 c_angle_deg 1.3 c_mcbond_it 1.18 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1769 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing