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Human N-myristoyltransferase (NMT1) with Myristoyl-CoA co-factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IU1 PDB ENTRY 3IU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 22.5% PEG 4000, 5 MM NICL2, 100 MM NA CITRATE PH 4.5, 2.5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.74 α = 90 b = 178.48 β = 90 c = 58.55 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 CCD ADSC CCD 2011-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.64 72 98.2 0.07 17.7 7.1 98990 2
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 1.64 1.67 85 0.71 2.4 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 PDB ENTRY 3IU1 1.64 89.24 93991 4944 97.91 0.1726 0.17008 0.1691 0.22157 0.2206 RANDOM 21.957
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] 1.29 -0.21 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 16.858 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 6.614 r_scbond_it 3.155 r_mcangle_it 3.013 r_angle_refined_deg 2.26 r_mcbond_it 2.09 r_chiral_restr 0.189 r_bond_refined_d 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 16.858 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 6.614 r_scbond_it 3.155 r_mcangle_it 3.013 r_angle_refined_deg 2.26 r_mcbond_it 2.09 r_chiral_restr 0.189 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 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_refined 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 802 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing