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Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A catalytic residue mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LX3 3lx3, ligand removed and with E37 mutated to A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 2 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.75 α = 90 b = 131.75 β = 90 c = 74.24 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 MARMOSAIC 325 mm CCD 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 1.9 50 99.8 0.079 12.9 9.3 19474 5 43
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) 1.9 1.97 100 0.683 2.4 9.4 1947
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 FOURIER SYNTHESIS THROUGHOUT 3lx3, ligand removed and with E37 mutated to A 1.9 35.3 19465 1011 99.68 0.198 0.196 0.2026 0.225 0.2337 RANDOM 49.913
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] -2.45 -1.22 -2.45 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.27 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 6.283 r_scangle_it 5.07 r_scbond_it 3.354 r_mcangle_it 2.892 r_mcbond_it 1.976 r_angle_refined_deg 1.243 r_angle_other_deg 0.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.27 r_dihedral_angle_4_deg 22.495 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 6.283 r_scangle_it 5.07 r_scbond_it 3.354 r_mcangle_it 2.892 r_mcbond_it 1.976 r_angle_refined_deg 1.243 r_angle_other_deg 0.806 r_mcbond_other 0.642 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing