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Structure of Plasmodium falciparum IMP-nucleotidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M Tris pH 8.5, 8% (w/v) PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.96 α = 90 b = 204.07 β = 90.02 c = 149.28 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 PIXEL DECTRIS PILATUS 6M 2015-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.973 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.6 48.34 91.7 0.99 7.5 3 250293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 3.18 0.82
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6RMD 2.6 48.3 1.83 250293 13486 91.71 0.2359 0.2298 0.2084 0.253 0.2164
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 19.975 f_angle_d 0.484 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51136 Nucleic Acid Atoms Solvent Atoms 1305 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing