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Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in complex with xanthopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A0S 2a0s, A chain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 298 2 ul 5 mg/ml protein (refolded in SGPP buffer + 0.01 mM Zn2+) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 10 mM MgCl2, 1 mM TCEP, 2 mM xanthopterin; cryoprotected by 3 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 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.358 α = 90 b = 131.358 β = 90 c = 73.577 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 2009-06-18 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 1.55 50 99.6 0.057 12.8 9 35343 4 28
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) 1.55 1.61 96.3 0.762 1.8 6.5 3414
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 2a0s, A chain 1.55 37.12 35342 1835 99.55 0.15 0.149 0.1604 0.167 0.1767 RANDOM 25.948
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] -0.95 -0.47 -0.95 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.795 r_dihedral_angle_4_deg 20.364 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 6.475 r_scangle_it 6.269 r_scbond_it 3.97 r_mcangle_it 2.871 r_mcbond_it 1.783 r_angle_refined_deg 1.676 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.795 r_dihedral_angle_4_deg 20.364 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 6.475 r_scangle_it 6.269 r_scbond_it 3.97 r_mcangle_it 2.871 r_mcbond_it 1.783 r_angle_refined_deg 1.676 r_angle_other_deg 0.939 r_mcbond_other 0.605 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1396 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling