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Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000081
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 30% PEG 1500, 0.2 M NACL, 0.1 M NA CACODYLATE, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.23 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.86 α = 90 b = 90.87 β = 111.92 c = 53.2 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 2M 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 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 1.4 40 94.6 0.044 17.7 4.3 78331
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 1.4 1.42 88.4 0.157 6.8 4.5
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 FOURIER SYNTHESIS THROUGHOUT 4CGP 1.4 39.92 74413 3918 94.52 0.15704 0.15565 0.1559 0.18408 0.1841 RANDOM 15.177
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] -0.1 0.08 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 20.674 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.522 r_long_range_B_refined 5.294 r_scbond_it 2.554 r_mcangle_it 2.491 r_angle_refined_deg 2.155 r_mcbond_it 1.672 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 20.674 r_dihedral_angle_3_deg 14.922 r_dihedral_angle_1_deg 6.522 r_long_range_B_refined 5.294 r_scbond_it 2.554 r_mcangle_it 2.491 r_angle_refined_deg 2.155 r_mcbond_it 1.672 r_chiral_restr 0.126 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 3354 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing