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Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 25)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B10 PDB ENTRY 4B10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M AMMONIUM SULPHATE, 24-26% PEG 3350, 0.1 M BISTRIS PH 6.0 - 6.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.32 α = 90 b = 119.13 β = 90 c = 178.46 γ = 90
Symmetry Space Group P 21 21 21
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 2011-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.58 37 98.4 0.1 14.2 7.9 163266 2
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 1.58 1.62 97.6 0.63 2.9 7.7
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 4B10 1.58 37.51 155636 8223 98.28 0.24027 0.23758 0.2359 0.29113 0.2887 RANDOM 16.261
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] -1.36 0.72 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.423 r_dihedral_angle_4_deg 16.324 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.842 r_angle_refined_deg 2.634 r_chiral_restr 0.15 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.423 r_dihedral_angle_4_deg 16.324 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.842 r_angle_refined_deg 2.634 r_chiral_restr 0.15 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9408 Nucleic Acid Atoms Solvent Atoms 1153 Heterogen Atoms 290
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing