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Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 15% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 5.6, vapor diffusion, sitting drop, temperature 291K 2 VAPOR DIFFUSION, SITTING DROP 6 291 14.55% PEG-4000, 0.2M ammonium acetate, 0.1M sodium citrate, 1:100 (w/w) chymotrypsin and 0.005M ADP., pH 6.0, vapor diffusion, sitting drop, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.946 α = 90 b = 127.946 β = 90 c = 127.247 γ = 120
Symmetry Space Group P 31 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 100 CCD MARMOSAIC 300 mm CCD 2007-11-29 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97926 APS 23-ID-B 2 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
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 1,2 2.84 30 100 0.089 12.9 11.1 29072
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) 1,2 2.84 2.94 100 0.978 10.5 2860
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.84 30 28742 1071 99.653 0.207 0.205 0.2589 0.245 0.2913 THIN SHELLS (SFTOOLS) 24.804
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] 0.212 0.106 0.212 -0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.173 r_dihedral_angle_4_deg 15.853 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 4.387 r_scangle_it 1.559 r_mcangle_it 1.452 r_angle_refined_deg 1.131 r_scbond_it 0.942 r_angle_other_deg 0.868 r_mcbond_it 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.173 r_dihedral_angle_4_deg 15.853 r_dihedral_angle_3_deg 12.927 r_dihedral_angle_1_deg 4.387 r_scangle_it 1.559 r_mcangle_it 1.452 r_angle_refined_deg 1.131 r_scbond_it 0.942 r_angle_other_deg 0.868 r_mcbond_it 0.818 r_mcbond_other 0.114 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5885 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling