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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, HANGING DROP 4.5 293 24% PEG 4000
5 mM NiCl2
0.1 M Na citrate
5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.53 α = 90 b = 58.29 β = 92.52 c = 153.9 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 IMAGE PLATE MAR scanner 345 mm plate 2017-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54179
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 2.05 16.8 99.3 0.139 0.164 0.085 0.99 6.2 3.6 51372 22.05
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 2.05 2.1 99.6 0.68 0.798 0.414 0.636 1.9 3.6
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 6FZ5 2.05 16.8 48702 2670 99.19 0.23876 0.23657 0.2357 0.27786 0.2727 RANDOM 32.57
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] 1.95 -0.3 -3.66 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_4_deg 12.966 r_dihedral_angle_3_deg 12.301 r_dihedral_angle_1_deg 6.345 r_long_range_B_refined 3.803 r_long_range_B_other 3.803 r_scangle_other 1.773 r_mcangle_it 1.679 r_mcangle_other 1.679 r_angle_refined_deg 1.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.367 r_dihedral_angle_4_deg 12.966 r_dihedral_angle_3_deg 12.301 r_dihedral_angle_1_deg 6.345 r_long_range_B_refined 3.803 r_long_range_B_other 3.803 r_scangle_other 1.773 r_mcangle_it 1.679 r_mcangle_other 1.679 r_angle_refined_deg 1.446 r_scbond_it 1.161 r_scbond_other 1.161 r_mcbond_it 1.069 r_mcbond_other 1.067 r_angle_other_deg 0.911 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 5976 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling xia2 data reduction PHASER phasing Coot model building