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Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.4M Sodium phosphate buffer, 17.5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.918 α = 90 b = 177.285 β = 90 c = 58.298 γ = 90
Symmetry Space Group P 21 21 2
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 2014-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 80 98.6 0.067 0.043 0.998 15.2 6.5 145112 12.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 96.6 0.814 0.557 0.766 2.1 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5O6H 1.45 80 136923 7227 97.83 0.21502 0.21346 0.2134 0.24416 0.2444 RANDOM 20.092
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] 2.56 -0.81 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.884 r_dihedral_angle_4_deg 21.128 r_dihedral_angle_3_deg 15.099 r_dihedral_angle_1_deg 6.336 r_long_range_B_refined 5.422 r_scbond_it 2.694 r_mcangle_it 2.622 r_angle_refined_deg 2.351 r_mcbond_it 1.951 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.884 r_dihedral_angle_4_deg 21.128 r_dihedral_angle_3_deg 15.099 r_dihedral_angle_1_deg 6.336 r_long_range_B_refined 5.422 r_scbond_it 2.694 r_mcangle_it 2.622 r_angle_refined_deg 2.351 r_mcbond_it 1.951 r_chiral_restr 0.163 r_bond_refined_d 0.024 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 6281 Nucleic Acid Atoms Solvent Atoms 820 Heterogen Atoms 222
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing