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Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-917
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.4M Sodium phosphate buffer, 17.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.138 α = 90 b = 178.852 β = 90 c = 58.465 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 2013-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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 1.29 89 99.1 0.062 0.039 0.999 14.7 6.2 206823 9.7
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 1.29 1.31 93.1 0.651 0.595 0.697 1.6 3.4
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 4c2y 1.29 55 195765 10300 98.68 0.16533 0.16384 0.1638 0.19348 0.1934 RANDOM 17.134
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] 1.7 -0.57 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.518 r_dihedral_angle_4_deg 18.794 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.437 r_long_range_B_refined 5.269 r_scbond_it 2.823 r_angle_refined_deg 2.498 r_mcangle_it 2.483 r_mcbond_it 1.685 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.518 r_dihedral_angle_4_deg 18.794 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.437 r_long_range_B_refined 5.269 r_scbond_it 2.823 r_angle_refined_deg 2.498 r_mcangle_it 2.483 r_mcbond_it 1.685 r_chiral_restr 0.175 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 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 6272 Nucleic Acid Atoms Solvent Atoms 1018 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing