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Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)
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 = 57.47 α = 90 b = 121.92 β = 90 c = 178.25 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 CCD ADSC QUANTUM 315 2011-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.79 55 100 0.11 14.5 7.2 118372 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 1.79 1.84 100 0.66 3 7.2
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 1.79 54.76 112339 5949 99.92 0.18767 0.18498 0.185 0.23856 0.2383 RANDOM 17.198
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] -0.79 0.46 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.575 r_dihedral_angle_3_deg 15.032 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_1_deg 6.58 r_angle_refined_deg 2.113 r_chiral_restr 0.157 r_bond_refined_d 0.022 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 37.575 r_dihedral_angle_3_deg 15.032 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_1_deg 6.58 r_angle_refined_deg 2.113 r_chiral_restr 0.157 r_bond_refined_d 0.022 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 9411 Nucleic Acid Atoms Solvent Atoms 1128 Heterogen Atoms 316
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing