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Crystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AU9 PDB ENTRY 3AU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 The protein solution containing 10 mg/mL PfDXR, 2 mM inhibitor, 3 mM NADPH, 2 mM MnCl2, 2 mM DTT, 50 mM Tris, pH 7.8 was mixed with an equal volume of the reservoir solution of 0.1 M Tris, pH 8.0, 20% PEG 3350, 0.3 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.36 α = 90 b = 77.28 β = 91.5 c = 109.41 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 93 IMAGE PLATE RIGAKU RAXIS HTC Mirrors 2011-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.3 51.34 89.2 0.064 15.6 3.9 34047 32.94
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 2.3 2.42 64.8 0.125 6.9 3.2 3590
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 PDB ENTRY 3AU9 2.3 44.64 34035 1698 89 0.23 0.23 0.2301 0.273 0.2732 RANDOM 37.3
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] -3.79 -5.39 -0.92 4.71
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 3.05 c_mcangle_it 2.24 c_scbond_it 2.12 c_mcbond_it 1.36 c_angle_deg 1.3 c_improper_angle_d 0.88 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6600 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 193
Software Software Software Name Purpose StructureStudio data collection PHASER phasing CNS refinement MOSFLM data reduction SCALA data scaling