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Crystal structure of Plasmodium vivax putative farnesyl pyrophosphate synthase (Pv092040)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YHK PDB ENTRY 1YHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 297 22% PEG 3350, 200 MM LI2SO4, 100 MM TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.969 α = 90 b = 116.39 β = 116.01 c = 92.416 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ M 2006-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 99.1 0.054 0.054 17.5 4.7 92263 92263 43.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 96.6 0.564 0.564 2.53 4.4 4429
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 PDB ENTRY 1YHK 2.1 20.99 92263 92136 1850 99.9 0.2291 0.2291 0.2285 0.2339 0.2615 0.2684 RANDOM 46.29
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] 0.151 0.9022 0.1029 -0.2539
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 0.92 o_bond_d 0.011 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation o_angle_deg 0.92 o_bond_d 0.011 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d o_improper_angle_d_na o_improper_angle_d_prot o_mcbond_it o_mcangle_it o_scbond_it o_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10961 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 45
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing Coot model building BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling