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Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with Imm-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 0.2 M Lithium Citrate, 30% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 4.61 73.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.765 α = 90 b = 155.765 β = 90 c = 102.612 γ = 120
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 2006-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.74 30 99.3 0.09 9.9 6.2 37032
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.85 99.9 0.534 6.2
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 (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 2.74 7.99 35515 35515 1781 99.1 0.17 0.17 0.1987 0.225 0.2423 RANDOM 60.8
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.87 r_dihedral_angle_4_deg 23.009 r_dihedral_angle_3_deg 20.945 r_dihedral_angle_1_deg 7.596 r_mcangle_it 2.5 r_scangle_it 2.243 r_angle_refined_deg 2.242 r_mcbond_it 1.513 r_scbond_it 1.487 r_nbtor_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.87 r_dihedral_angle_4_deg 23.009 r_dihedral_angle_3_deg 20.945 r_dihedral_angle_1_deg 7.596 r_mcangle_it 2.5 r_scangle_it 2.243 r_angle_refined_deg 2.242 r_mcbond_it 1.513 r_scbond_it 1.487 r_nbtor_refined 0.345 r_nbd_refined 0.297 r_symmetry_hbond_refined 0.256 r_symmetry_vdw_refined 0.24 r_xyhbond_nbd_refined 0.224 r_chiral_restr 0.157 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5283 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 82
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing