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Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.16 293 0.11 M (NH4)2SO4, 15.5% PEG4000 0.1 M, 5% Jeffamine M-600, Sodium Acetate/ Acetic Acid pH 4.16
Crystal Properties Matthews coefficient Solvent content 3.25 62.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.994 α = 90 b = 203.089 β = 121.07 c = 82.165 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2014-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.37 41.85 99.22 0.1 8.96 3.8 51893
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 2.37 2.51 88.9 0.502 2.58 2.11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1TZS 2.37 41.85 1.35 51858 1990 99.16 0.1811 0.1794 0.1848 0.2237 0.2265 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.972 f_angle_d 1.159 f_chiral_restr 0.048 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6386 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 168
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing