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C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): ternary complex with coenzyme A and GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AG7 PDB ENTRY 4AG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 MM ACCOA, GLCN-6-P, GLCNAC AND 0.1 M TRIS-HYDROCHLORIDE PH 8.5, 0.2 M SODIUM ACETATE TRIHYDRATE AND 30% (V/V) PEG 3350 AND 11 MM BACL2
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.872 α = 90 b = 53.353 β = 90 c = 135.096 γ = 90
Symmetry Space Group P 21 21 21
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 2005-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.75 20 98.1 0.05 28.1 3.6 34633 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 1.75 1.81 89.5 0.26 3.5 3.1
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 4AG7 1.76 14.99 33878 715 97.09 0.19124 0.19042 0.1887 0.23216 0.2119 RANDOM 31.121
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 17.297 r_dihedral_angle_3_deg 14.289 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 2.289 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 17.297 r_dihedral_angle_3_deg 14.289 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 2.289 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 2580 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing