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Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 24% PEG 4000
5 mM NiCl2
0.1 M Na citrate
5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.278 α = 90 b = 58 β = 92.18 c = 153.309 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 110 PIXEL DECTRIS PILATUS3 6M 2016-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976251 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 76.6 84.9 0.1 0.129 0.08 0.981 4.5 1.9 46006 15.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 89.8 0.388 0.498 0.308 0.806 2.1 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6FZ5 2 50.87 43570 2392 84.46 0.20057 0.19865 0.23492 0.2697 RANDOM 27.798
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] 2.72 0.11 -2.19 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.507 r_dihedral_angle_4_deg 14.326 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 6.479 r_long_range_B_refined 3.501 r_long_range_B_other 3.499 r_scangle_other 2.121 r_mcangle_it 2.003 r_mcangle_other 2.002 r_angle_refined_deg 1.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.507 r_dihedral_angle_4_deg 14.326 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 6.479 r_long_range_B_refined 3.501 r_long_range_B_other 3.499 r_scangle_other 2.121 r_mcangle_it 2.003 r_mcangle_other 2.002 r_angle_refined_deg 1.456 r_scbond_it 1.339 r_scbond_other 1.339 r_mcbond_other 1.225 r_mcbond_it 1.224 r_angle_other_deg 0.922 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6094 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing Coot model building